All Good Things
by PapayaK
Summary: I really wanted to get this out before season 5 premieres because when it does, this will almost certainly become AU. I suppose it already is, a little bit, because in this story, we do not lose Shaw in the basement of the stock exchange. What if John disappeared instead? It will, ultimately, give one idea on the closure of the Samaritan timeline.
1. April 9

A/N - I really wanted to get this out before season 5 premieres because when it does, this will almost certainly become AU. I suppose it already is, a little bit, because in this story, we do not lose Shaw in the basement of the stock exchange.  
What if John disappeared instead?  
This story takes place sometime between "Control-Alt-Delete" (4x12) and "Asylum" (4x21) It will, ultimately, give one idea on the closure of the Samaritan timeline.

 **oO0Oo  
April 9th  
oO0Oo**

"Miss Shaw, I really must insist that you stop purchasing these 'cow femurs' for Bear."

"But he likes them, Finch."

"Yes - that may be. However _they_ do not like _him_. At least this particular brand. Perhaps you could try something organic?"

"Are you kidding? Organic? Organic just means it's got bugs in it, Finch."

"Then _something_ with fewer chemicals? It really does wreak havoc on his digestion."

"Well - then make Reese clean it up - Bear's his dog, after all… Where is Reese anyways?" Shaw looked around the subway - she hadn't seen Reese since their last case concluded a day and a half ago.

Finch glanced up from where he was watching Bear devour his latest toy and looked at her with some concern behind his gaze. "I'm not sure if he made you aware of it, Ms. Shaw, But Mr. Reese sustained some injuries in our most recent activities. With that on top of the fact that he's had very little opportunity for sleep over the last week, I requested that he take some down time to recover - at least until our next number."

Sameen frowned to herself. Reese _had_ managed to keep his injuries from her and she was usually pretty good about noticing such things. It was important to be aware of your teammates' battle readiness - especially now that Samaritan seemed more powerful than ever. It certainly wasn't because she _cared…_

She looked back at Bear, who appeared to be having the time of his life, and sighed. "I'll be more careful about reading labels in the future… okay, Finch?" When he didn't respond, she looked back at him. He was frowning at his phone. It seemed he had received a puzzling or worrisome text. "Finch?"

He kept frowning and held out the phone toward her. "I just received a text from Mr. Reese. It appears to be some kind of code, but I have to confess, I don't know what it means. Do you?"

She shrugged and took the phone from him. She looked at the screen. It held three seemingly random letters. They formed no word.

She gasped. She froze.

"Miss Shaw?"

Sameen stared at the screen of the phone. She knew exactly what those letters meant and it felt like a punch in the gut.

Which was strange. She didn't usually have reactions like this.

A punch in the gut. In a fight, she prepared for those and they barely left a bruise. But if someone managed to catch her unprepared… It hurt - it was a shock - and it left her gasping and nauseous - which was exactly how she felt right now.

Finch felt the first tendrils of panic grab at him when she did not respond to his inquiry but continued to stare, unmoving, at his phone. "Miss Shaw?!"

Miss Shaw didn't normally _do_ emotional reactions. The fact that he was clearly seeing one now caused him no end of worry. "Sameen." He prompted softly, but urgently. "What is it? What's happened?"

Shaw realized that Finch was waiting for an explanation of John's text, But she was loathe to give him one. She shook her head at how smart - and how _cruel_ John was to send _this_ text to Finch's phone; a text that only _she_ would understand. Her hand holding the phone dropped to her side and she stared at him. "Reese was burned by the Agency, right?"

Finch blinked. "You could say that..."

"So you know what that means."

He tilted his head, worried. "The Agency basically turns their back on you. You are 'fired' in the most graphic of ways - forgotten - abandoned… it nearly always means the agent has been - or will be - captured... or... killed… In John's case it was the latter. The Agency tried to wipe him off the face of the planet." He was becoming increasingly uncomfortable with the course of this conversation. He very nearly didn't ask, "Why?" He was pretty sure he didn't want to hear what she was going to say.

She held up the phone towards him. "Are you _absolutely_ _ **sure**_ this is from Reese?"

"It is from his phone, yes…"

Her arm and her eyes fell. "Then... we've lost him." She said- her voice completely without emotion.

He took one step toward her. "What do you mean… _lost him_?"

She looked down at the phone in her hands and spoke quietly. "This is a burn code." She was surprised that she needed to pause and swallow before explaining. "It's something an agent will set up with his team. It is a way to… 'burn' yourself... If the situation warrants it - if you know _absolutely_ that you _cannot_ survive or be saved - and any attempt at rescue would be suicide - you can… 'burn' yourself." She swallowed. "This is John's burn code. He's telling us he's not coming back and not to come after him... that he's lost to us - that something has happened and _we cannot save him_."

Finch could not accept the information being shared with him. "That's ridiculous." He said dismissively. "It's someone else using John's phone - trying to throw us off - we have to find him!"

"Finch." Shaw rested a hand on his arm as he quickly sat and began to type. "It's not. It's John."

"How can you be sure?"

"Because he set the code up with me. He and I are the only two people in the world who even know the code _exists_ \- much less what it is. And if you think someone managed to trick him into sharing it? Or tortured it out of him? No way. It's from John."

Finch's eyes were darting back and forth - he was very nearly in a true panic. "He _knows_ we won't listen - that we'll come after him anyway - that's what he did with me. More than once I gave him every reason - I _tried_ to keep him from coming after me and rescuing me. _Nothing_ stopped him... _Nothing_ will stop _us_ now." The purpose gave him some measure of calm and Sameen hated to crush it.

The truth was she was feeling conflicted. On the one hand she knew John hadn't sent the code lightly. He would not have sent it unless he truly believed it was necessary - and John was usually right about such things. On the other hand - she was just as desperate to go after him as Finch. If it was just her, she would already be gone, but she also owed it to John to make certain that Finch was safe.

She decided on something of a compromise.

"Harold." She pulled up the opposite chair and sat facing him. As much as she hated it, she had to get him to listen. "You're right. John knows you won't stop looking for him. That no matter how dangerous he tells you it is, you'll try anyway and probably get yourself killed. No - actually - In light of this code - you _would_ get yourself killed. And probably me too - _and_ Root - Fusco - Bear… _Anyone_ we involve. That's why this text isn't _really_ directed at you at all... It's a message _to me_."

The last sentence was spoken with such despair that Harold finally stilled and really listened to her.

She was glad to see it - but also saddened. When she spoke, she couldn't meet his eyes. "Finch - you _know_ how much I hate to admit it, but overall- Reese is better than me. He's more skilled in many aspects of our work." She looked up at him. "And he knows _us…_ knows my training, what I can and cannot do. And he is telling us that this is beyond our skills. Whatever it is - we can't beat it. And yes - he knows we'll try anyway." She cleared her throat. "By sending a message to ME on YOUR phone… He's asking me to keep you from trying."

"But you won't do that - you will not abandon him…" Finch implored her.

But she leaned forward and looked him in the eye evenly. "Yes. Finch. I will." She held up the phone once more. "This is a last request, Finch. This is a request from a dying man - from a _friend_. I owe him. You can bet your life I will honor it. And betting your life is exactly what you would be doing if you cross me."

"Sameen…" Finch was beginning to see that she was actually serious.

Knowing she had him listening, she gave him some hope. "But that does not mean we are going to forget him." Shaw continued. "We can't launch a rescue mission right now, but we aren't going to sit on our hands either. We can start by trying to figure out what happened.  
I'm sure his phone's been destroyed by now, but where was he when he sent this?"

Finch stared at her for a split second before leaping into action. It only took him a moment to pull up the GPS records on John's phone. "The text was sent from his apartment."

"Let's go."

oO0Oo

Finch and Shaw arrived at John's apartment in record time and Shaw entered warily, gun drawn and ready, Bear at her side. Finch followed cautiously.

They found absolutely nothing. John's apartment was neat and quiet. There was no sign of a struggle, no clue as to what might have happened.

Shaw holstered her weapon.

"What now?" Finch asked.

She sighed. She'd really hoped they would find _something_ to let them know if he was even still alive. "I'll take a spin around the neighborhood with Bear. See if he can pick up a scent. You head back and work your computer magic. See if you can hack security feeds around the building… you know the drill."

He nodded, discouraged and worried, and left.

Finch had known from the very beginning. ""We'll both wind up dead… really dead this time." But to have his prediction come true was far more painful than he'd expected. And to have it come true _now_ \- when things were the darkest they'd ever been. When Samaritan was growing in power every day… If John was really dead, then Finch feared it would not be long before the rest of them followed.

A few hours later they were both back. Neither of them had found anything useful. Even Bear had found no trace of his scent outside his apartment building. It seemed that John had simply disappeared.

"Do you believe he is alive?" Finch asked her in a small voice.

She gritted her teeth. "If it is humanly possible to survive. John will. We need to hold onto that." She looked at Finch, suddenly feeling more alone than she had in a long time. "And we will not stop looking." She also felt a new sense of resolve. John had always been the protector, where she had been something of a loose cannon - allowed to be so by the very stability John provided. That would change now. She would protect Finch, and their mission, with the same fierceness John had.

She silently made her vow to him - wherever he was.

 **oO0Oo**

 **TBC…  
oO0Oo**

Please feed the writers - they're always starving for reviews!


	2. April 27th

**oO0Oo**

 **April 27th  
oO0Oo**

After that night - everything was different.

Finch had eventually gone home but he hadn't slept. He had spent the long, dark hours wondering what could possibly have happened to John. Was he alive or dead? Was he suffering? Was he waiting for rescue? Harold was a man who survived on a steady diet of facts and information. The not knowing - not being able to act - to help his friend - was killing him.

On a more practical note, he was also trying to imagine continuing their work _without_ John.

He couldn't do it.

And yet he knew that morning would come. Sooner or later they would receive another number and life would go on. Whether he wanted it to or not.

In the morning he had returned to the subway. An hour later they had received two more numbers. He and Shaw had just looked at each other for a long minute. And then they had gotten to work.

oO0Oo

Both Finch and Shaw spent every spare moment of the days following trying to learn what had happened. They kept their promises to each other to never give up hope, to never stop looking - but there seemed to be absolutely no trace.

Without him, everything become more dangerous. Everything had to be planned two or three times more meticulously. They lost more numbers than ever before. There was no more swooping in at the last moment to rescue someone.

After a few days, Fusco had finally complained about his partner's absence - only to be told what had really happened. At first he hadn't believed that they really had no idea. But when he finally became convinced, an honest to goodness 'missing persons' case was opened in Detective Riley's honor. It turned up no leads.

With the added danger Samaritan presented, Finch was finally forced to do something he _never_ thought he'd do: If a number appeared too dangerous, if the person put them too close to Samaritan' all-seeing eye, he didn't even try. He turned his back. He simply could not afford to lose anyone else. It didn't happen often, but every time it did, he died a little inside.

After a week the stress began to show in all of them. They snapped at each other. Bear refused to eat.

The team had been dealt a blow from which they might never recover.

oO0Oo 

A young man in a white lab coat entered Greer's presence and waited to be acknowledged.

Finally the older man turned and faced him. "Ah, Doctor Sievert. You have information for me?"

The doctor approached. "Our latest acquisition is proving to be quite difficult."

Greer raised an eyebrow and turned to face the young man directly. "Are you referring to Detective Riley?"

Doctor Sievert nodded. "He fights the process like no one ever has. And he has managed to escape once." He quickly continued. "He was immediately… apprehended."

Greer frowned. "Are you here to report failure?" He asked ominously. "Given _who_ Detective Riley is, it is imperative that you _not_ fail."

"No, Sir!" The doctor answered with fear in his voice. "I merely need authority before taking the sessions to the next level. Those techniques are not to be used without prior approval."

Greer simply nodded, smiling a bit. "Please - by all means - be as brutal as you need to be." He responded drily. "The good detective will come to see things from Samaritan's perspective… or he will die."

The doctor nodded and left.

 **oO0Oo  
TBC…  
oO0Oo**


	3. May 10th - June 5th

oO0Oo  
May 10th  
oO0Oo

After nearly a month of silence, Root showed up.

She already knew. She said (somewhat dismissively in Finch's opinion) that the machine was doing everything possible to find John as well. Root was _fairly_ certain that Samaritan was involved - but if it _was_ Samaritan, then why weren't they _all_ being hunted? Their carefully crafted, false identities were like dominoes - if one was discovered, the likelihood of all of them being discovered increased tenfold - a hundredfold. But they seemed to be undetected - so who had taken John? Who else could possibly be capable of not only taking him and keeping him this long?

Of course the fact that he might already be dead weighed heavily on all of them, but they held on to hope and did not speak of possibilities.

Elias was contacted and was genuinely dismayed to hear the news. He promised to watch for signs of John and to let them know if he heard anything. But he also couldn't help being pleased that his illegal activities had lost their most formidable foe.

Shaw began to encourage Finch to start looking for a replacement. He'd never find someone as talented and perfectly suited for their mission as John, but surely there was _someone…_ She even offered to go through a list of her former associates… Finch shut her down every time. It was just too dangerous now, to involve anyone else. And Finch knew John himself would never condone it.

oO0Oo  
June 1st  
oO0Oo

Late one night, Shaw was attempting to get a Number safely out of a building that was full of enemies. Fusco was waiting at a back entrance, but there were five gunmen between her and freedom. Once again she found herself wishing that John was there. Not that she wasn't perfectly capable on her own, but… oh who was she kidding? She missed him.

Just then an increase in gunfire tore her mind back to the present. Someone else had come to join her side. Had Fusco taken the initiative to come in after her? But it was Root.

"Wow. I just never know where you're going to show up." Shaw groused as she grabbed the number's arm and dragged him towards Fusco.

"Hi sweetie." Root flirted. "Did you miss me?"

Shaw sighed. "You're not here just to help this guy." She shook the man's arm and propelled him towards the back door. "So why are you here?"

Root's smile fell. "It's about John. She finally told me something."

Shaw watched as the guy opened the door. Fusco was there and took him into custody, and throwing a nod in their direction, disappeared.

"I'm afraid it's not good."

"Of course not. If it was good news, you'd be telling Harold instead of me."

"She was able to confirm that Samaritan has him."

"Big surprise…" Shaw dead-panned.

Root looked away as she concluded, "They're trying to brainwash him."

Shaw snorted. "Yeah - like that'll work. Do you have any idea the kind of training he's had in resisting that? Not to mention his own natural stubbornness…"

Root sighed sadly. "And have you thought about what resisting will do to him?"

Shaw just looked at her. Of course she had. She also knew that John would prefer death to joining Samaritan. "Let me guess. You want me to tell Harold."

"If you would, please. I have to be at work in less than an hour. I'm a bicycle messenger this week. It's really thrilling."

Shaw nodded sullenly and watched Root turn to leave.

But she paused and looked back. "I am sorry, Sameen. If there was anything we could do…"

"Yeah." Shaw replied. "Whatever."

How was she going to tell Harold that they had proof John was alive, and then crush him by explaining what was happening?

Good thing she didn't have any feelings.

oO0Oo  
June 4th  
oO0Oo

"Finch - I got nowhere else to go." Shaw whispered breathlessly.

"Miss Shaw, if you take that route you will be outside the Shadows. Samaritan will be able to see you."

"You want me to get this guy to safety or not? It's the only way. I'll only be off the map for a hundred yards. We just have to hope Samaritan is looking the other way."

"Miss Shaw, if saving this man puts you in Samaritan's sights, I would prefer… I would prefer that you leave him where he is and return to safety."

"Finch - that's not what I'm here for." She responded angrily.

But Finch pleaded with her. "If I lose you too…" He couldn't finish. And Shaw did not respond. Finch only heard the usual rustling noises, as Miss Shaw did what she'd set her mind to.

When he heard a frighteningly familiar 'phut!' noise he sat up straighter. "Miss Shaw?!" He'd unfortunately come to recognize the sound of a bullet hitting an inanimate object. And he was certain someone had just fired at Sameen and her charge, their latest Number. "Miss Shaw!"

And he sat through the agonizing silence until, "Yeah, Finch. We're good." She whispered breathlessly. "Someone took a shot at us, but they missed. Jimmy here is as good as out of the country. I'll check in soon." And with that she was gone.

oO0Oo  
June 5th  
oO0Oo

"Yo, Glasses." Fusco called early in the morning. "You know anything about a homicide on 61st? Kinda looks like your kinda thing."

"I'm not sure what you mean, Detective." Shaw's close call the night before had been on that street, but Finch knew of no deaths that were related to Jimmy Davis's flight from the city.

"Guy here… If I didn't know better I'd say it was a pro taken out by another pro. You don't know anything about that?"

Finch frowned. "I do not, but if you would care to send me what you have I will look into it." A strange feeling had begun to crawl up the back of Finch's neck. But he would have to see what Detective Fusco had before he could come to any conclusions.

Later that night, he asked Miss Shaw to join him in looking over the file. They both came to the same - unlikely - conclusion: The dead man had been found in a position that led them to believe he was the sniper who had taken a shot at Shaw and Jimmy - probably one of Samaritan's agents, as Jimmy's enemies didn't have that kind of firepower or talent.

But who had killed the sniper? The crime scene was absolutely clean - no weapons, no prints - no clues of any kind - which only served to reinforce the idea that someone very good at their job had killed this guy.

Finch spoke without meeting her eyes. "It certainly looks as if someone was protecting you."

"Finch…" She sighed. She'd love to believe that it was somehow John, too - but that was just crazy. "If it was him - why didn't he give us some kind of signal? Something… to let us know he's alive?"

At that he did look up at her. The hope in his eyes was almost enough to break her heart. "I have lost far too much to give up on John." He looked away and finished in a whisper. "Not without some kind of proof…"

oO0Oo  
TBC...  
oO0Oo


	4. June 19th

Special thanks to: **FlamMabel, IrrelavantSherlock512, Lady Sundiver, M_E_Lover, IrmoKementari, elaine0510, Fandom_Person_of_Interest_2015, kenorob1,** and **sandunder** for leaving comments.  
And special thanks to **Aussie_Muggle, Fandom_Person_of_Interest_2015 (Fandom_Person_of_Interest_2014), allapplesfall, IrrelavantSherlock512, dancing_dog, and LeggoMyEggoMeggo** as well as 15 guests for leaving Kudos on AO3.

 **oO0Oo**  
 **June 19th**  
 **oO0Oo**

"It's been a month, Finch. How long until you get serious about finding us some help?" She spoke as she bandaged a bullet graze on her arm. She'd just returned from delivering one of their numbers to the international terminal for a permanent trip out of the country and decided it was time Finch got serious about a new team member. She simply couldn't continue with just Fusco for back-up.

Finch didn't hear her. He was paying no attention to her because he was intent on printing something. "Miss Shaw!" His voice held the first bit of excitement Sameen had heard since that horrible night. "Look at this and tell me what you see." And he held out a blurry 8 x 10 shot from surveillance footage.

She took it patiently and studied it. It didn't take her long to see what had him excited. She pointed to a man in the photo. "You think this is John?"

Finch allowed a small, hopeful smile to pass over his features.

"Finch…" She nearly groaned - false hope could be devastating. "You don't know-"

"But look." Finch took the photo and pointed. "Look what he's doing… where he's looking… and then look at this."

He held out a second photo and pointed to the same person. The man was centered this time, and staring directly into the camera. It was still too blurry to make out the features, but he was the right height - the right coloring - _and he looked like John._

"Just tell me if you see anything that proves it's not him." Finch stated honestly.

She closed her eyes briefly and then looked at Finch. "This is just like the last time we thought we might have caught wind of him. If it **IS** him - why hasn't he contacted us? The man in the photo is fine - he's healthy - he's not being held against his will - if this is John - why isn't he here?"

Finch's face fell. Of course he had thought of that - but he looked up at Shaw. "What if this IS him contacting us? Letting us know he's still alive and on his way to us?"

"Okay, fine." She relented. "Where is this? Let's check it out."

And she was rewarded with Finch's first genuine smile in over a month.

"Let's go, Bear!"

oO0Oo

As it turned out, it was Bear who gave them the greatest hope.

The moment they reached the intersection where the man had been standing, Bear became hyper alert. He didn't bark, but he came to attention, his whole body trembling with excitement. He whined deep in his chest. Finch commanded him in Dutch to 'track!' and they were moving. Bear led them for ten blocks before finally losing the scent.

The three of them spent over an hour in the area where Bear lost the trail, but they found nothing.

"But you must agree," Finch insisted. "Based on Bear's reaction - it has to be him! He's alive!"

Shaw actually did agree - but the thought did not comfort her. "Finch… Like I said - he's a free man. Where is he? Why hasn't he found some way to contact us? Something!? If it is John - wouldn't he at least try?"

"But the photo…"

She knew Finch believed the photo was John trying to contact them, but she was too realistic for that. "Finch... We know Samaritan was trying to brainwash him… Behavioral engineering works, Finch, it just takes time. And they had John for well over a month… What if-"

Finch went still and spoke almost angrily. "Do not say it, Miss Shaw. To lose John in _that way?_ To have him alive - but no longer _him_? I won't believe it. I can't. You're the one who said he was even better than you - he's been trained to _resist_ brainwashing techniques - he wouldn't let them…" Finch's voice trailed off as he realized how desperate he sounded.

She just looked at him, not saying what they were both thinking - _over two months -_ had passed. Could _anyone_ hold out for that long against what were sure to be brutal efforts?

But Finch could not help but feel that if it were true - if they had really lost John - then Samaritan had already won.

 **oO0Oo**  
 **TBC…**  
 **oO0Oo**

A/N - Thanks for coming along for the ride. I'm posting this chapter early since it is rather short. Please leave a note and let me know what you think so far. Thanks! Papaya


	5. July 11th

A/N - Here is the promised action... **  
**

 **oO0Oo  
July 11th  
oO0Oo**

Everything changed once again late on a Tuesday night in July.

Shaw was working a number and had Finch in a nearby car as her back-up as Fusco had a double homicide and a new partner to break in. That was taking all his energy this week.

Then Root showed up to help. Shaw was surprised since this was one of their more straightforward cases in a while. Root usually only showed up for the crazy stuff. "What are you doing here, Root?" Shawn murmured as she watched their number from behind some bushes near the east river.

"I have no idea, Sameen." She'd responded cheerfully. "She rarely explains why these days. All I can tell you is that she was quite insistent." Root took a deep breath and looked up at the sky. "Nice night, though, for two girls to be out on the town..."

"Isn't it, just?" Came a gravelly whisper as two pistols were pressed into the back of their two heads.

It was John.

Both women weren't sure whether to celebrate or be terrified. John was there. He was whole. He was apparently unharmed. But he was also holding guns to their heads.

"Hi, Shaw. Hi, Root." He spoke calmly, but managed to sound more menacing than ever. Having gotten their attention, he retreated to a distance neither woman could cross quickly enough to take him. "I know exactly what you two are capable of, and if either of you twitches I will put a bullet in the other one's head."

"Nice to see you too, John." Shaw responded as she and Root slowly stood and turned to face him, their Number forgotten.

" _And_ I've got a sniper pointing an M82 Barret 50 Cal at your friend's head over there, so I suggest you ask him to join us... unless you want to see his brains splattered all over the dashboard of his car."

Both women watched John very closely - hoping - _praying_ that this was all some kind of act - that their entire team _hadn't_ just been captured by Samaritan… by John.

"John?" Shaw drew out the word, searching for some clue.

Instead he held up her phone - when he had taken it off her, she had no clue. Noticing her puzzlement, he commented with a slight smile. "I've had some further… um... _training_... since we last saw each other, Shaw - good stuff. You'd like it." His eyes flicked briefly in the direction of Finch's car. "Now call Finch and get him over here." He tossed the phone to her and she caught it.

Root attempted to get through to him. "John… please… you don't have to do this."

He laughed out loud - which both women found incredibly eerie. " _Far_ too late for that, Root." He shook his head with a smile. "Let's go." He gestured with his weapons to guide the women out into the open and onto the bridge spanning the river which was deserted at this hour of the night.

When Shaw didn't make the call, John prompted, sounding almost disappointed, "Shaw - do you really want me to give the green light?" He asked her.

"You won't kill Finch." She scoffed. "I _know_ you. You won't. You _can't_ "

But he looked at her with dead eyes that made her shiver in spite of herself. When he spoke, he sounded nothing like the friend she's grudgingly come to respect and everything like the monster he'd once been. "How badly do you want to test that theory?"

John was serious. That much was obvious. And Shaw realized that even if he was only pretending to be their enemy, he wanted Finch there. She frowned at him, trying to determine whose side he was really on. The chance that he was only faking was extremely slim - and getting slimmer by the moment. Especially when he signaled to the unseen shooter and they heard Finch's car window shatter, accompanied by a cry of fear from the man inside.

Both women spun to look at the car.

"That was just a warning." John told her as she turned back to stare at him angrily.

Without taking her eyes off his, she touched her earwig. "Finch. John's here. But before you celebrate the return of a friend - you need to know - he's no longer himself. The brainwashing worked."

There was no verbal response, but they all heard him get out of the car and begin his walk toward them.

John only chuckled. "You call it brainwashing - I call it being made to see the light. Samaritan makes a lot more sense than the Machine, Shaw."

"Yeah - right." She commented sarcastically.

Two other Samaritan agents- who seemed to be taking orders from John - appeared and helped herd their little group out onto the bridge where Greer was waiting.

Finch was made to join them there. "John!" He couldn't help exclaiming as he walked right up to his former partner. "I am exceedingly pleased you are alive!"

John only glared and Shaw saw he was about to hit the smaller man so she stepped between them and took the punch.

She went down hard. John wasn't pulling his punches. If he'd succeeded in hitting Harold, the man would not have gotten up easily. But Shaw spit a mouthful of blood and stood - glaring at the man who was no longer her friend.

Harold stared at both of them - absolutely brokenhearted. "John…" he whispered.

He was ignored.

Then Greer spoke. "I am _so_ pleased we've had this opportunity to show you how effective our techniques can be. Mr. Reese has proved to be an excellent asset and it is truly poetic that _he_ be the one to end your feeble resistance." Greer smiled at the three of them. "Do you know _he_ was the one tasked with hunting you? _He_ put the team together tonight to take you down. _He_ chose the method of your execution. _He_ is the one who will carry it out. And I must say, I approve. The river is at its highest and fastest current here. Your bodies will, most likely, never be found." Greer walked over to stand in front of Finch who could not take his eyes off John. "I wish we had more time to get to know one another. I once considered you the most important man in the world. Ah well. You have absolutely no more reason to exist. Good-bye." Then he turned to Reese. "Mr. Reese - at your convenience." And with that, Greer began to walk towards his waiting car.

"John - don't let Samaritan win… please..." Finch pleaded one last time, but John only looked at him with something between disdain and disinterest.

Then John gestured briefly, and the two men who were assisting him lined the three prisoners up against the railing of the bridge. Finch could hear the cold water rushing past beneath them.

John and Finch regarded each other for a long moment. Finch was forlorn, but _desperately_ imploring. In John's eyes he saw only death. But then... was there a twitch? a glimmer?

He had no time to see he was right because suddenly, things happened very quickly.

John fired three times, shooting each of them in rapid succession. There was one large, prolonged splash that was caused by three bodies hitting the water at nearly the same time.

oO0Oo  
TBC…  
oO0Oo

A/N - I know. I can't believe it either!


	6. July 11th cont'

You survived the cliffhanger 8-0 - Here's your reward. :-)

 **oO0Oo**  
 **July 11th cont'**  
 **oO0Oo**

Shaw was the biggest threat and John shot her first - one bullet straight to the heart. Root was next and Finch had the space of a single heartbeat to watch both women fall before he felt a searing pain and then the pull of gravity as he too, went over the railing.

He hit the water. It was very cold and extremely loud. Polluted water filled his eyes and mouth and he felt himself sinking. The pain of the bullet wound was nearly obscured by the horror of being killed by his best friend.

But then- to his surprise - two small but strong arms were wrapped around him and he felt himself being pulled. His head broke the surface and he spluttered and gasped. Finally he realized that he was being questioned. "-you swim? Finch! Finch! You with me? Can you swim?!" Shaw was urgently whispering in his ear.

In his state of pain, desperation and utter confusion he could only answer: "I used to…"

"Then float!" She whispered urgently. "Lay on your back and float. Let the current take you - Root's unconscious." And she was gone.

Gradually, Finch's mind began to clear. He was shot, but he was alive and he was being pulled rapidly downstream. They were already far from the bridge. He saw part of an old piling standing up in the water and managed to drift toward it, grab it and hold on with his one good arm. It was slimy and slippery but he wrapped himself around it as best he could and thought about the fact that John Reese was an _extremely accurate marksman_ and if he had _meant_ to kill at a distance of mere feet he _would not have missed._

Finch looked upstream and saw what looked like no more than a piece of driftwood heading his way, but he knew it was Shaw holding Root's head above water. He sought a better spot on the pilings and hissed at her. She spotted him immediately and struck out with strong strokes toward his perch.

When she reached him, she spared a small nod of approval of what he'd found. The pilings were remnants of some old pier. While there were enough pieces above water to give them something to hold onto, there wasn't enough to make them overly visible to anyone who might come looking. "Good job, Finch. Can you hold Root here? I think she hit her head when she went over." She knew it must be incredibly difficult, not to mention painful to maneuver his body under these circumstances. It was hard enough to _walk_ with a fused spine, much less climb and cling, monkey-like, to a slippery piece of wood.

Finch nodded and tried his best to help get Root into a semi-secure position in spite of the fact that his left arm was quickly becoming numb. Thankfully, Root chose that moment to begin to stir.

Shaw kept looking over her shoulder at the water.

Finch was still trying to understand what had happened. "What are you looking for?" He asked as he helped a groggy Root to grab onto a piling with her good arm.

Shaw didn't take her eyes off the river but spoke quickly over her shoulder. "John shot me in the chest because he knew I'd be wearing a vest." She huffed out a quick laugh. "I wondered why he had a .22..." She shook her head, still watching the river. "He shot me first because no one would watch where he shot you two after that. He got Root in the shoulder and you in the arm. And Greer was right - he dropped us where nobody's gonna look for a body." Then she turned and positively grinned at Finch. " _He had no intention of killing us, Finch._ He beat 'em! All this time… he's been playing them." Then the smile fell. "The problem is - they won't extend _him_ the same courtesy. As soon as he killed us - they've got no more use for him. You can bet he went into the water after us - and he won't be nursing a graze - there he is!"

And she dove into the current and began fighting her way towards an unmoving shape floating swiftly downriver.

By this time, Root was fully awake and the two of them fought for more stable positions and prepared to help Shaw with John. He was quite a bit bigger than she, he was dead weight and the current was strong. She was nearly exhausted by the time she managed to pull him close enough for them to grab.

"We gotta... get him... to shore... I don't… I don't think he's breathing." She gasped.

And so as quickly and carefully as they could they slid themselves and John from piling to piling until the water was shallow enough that they could stand. They dragged him halfway onto the shore and Shaw collapsed - utterly spent. Root bent over John, trying to asses the damage to his chest, and Finch reached into a pocket, hoping that there was a chance that his phone had survived. It hadn't.

He almost gave up right then until he saw Root talking urgently to an unresponsive John. "No you don't, John. Not after all this. You didn't survive all of that to die now! We aren't losing you!" And she began CPR.

Finch looked up, searching for some way - any way to call for help. All he saw was a rather seedy, broken-down shack nearby, but it just might have a phone. He dragged himself to his feet, clasped a hand tightly over the wound on his arm, and stumbled over to it. It wasn't locked and was very nearly empty. Clearly a haven for the homeless, it was vacant and void of anything useful.

Finch felt desperation overtaking him. Root was correct. John had somehow managed to - not just resist Samaritan's brainwashing - but to trick them into believing that it had worked so that he could have a chance at saving the rest of them. And now he was dying. He left the shack and searched the area once again for any sign of hope.

Somewhere, a phone began to ring.

Finch turned in the direction of the sound. He couldn't see anything, but he began limping in that direction. Was the machine giving him a number… _now_?! He came around the edge of a building and saw a pay phone on the other side of a parking lot.

Just when he reached it, it stopped ringing.

He stared, his hand still raised to answer.

As he stood there, the phone was suddenly lit up as a car pulled into the lot where Finch stood. He turned and stared at it, terrified. Had Greer come looking for them after all?

The car stopped just feet from him and someone got out. Finch squinted.

"My name is Michael Sievert. I'm a doctor. Or at least I used to be. I got a text telling me to come here."

 **oO0Oo**  
 **TBC...**  
 **oO0Oo**

Did anyone notice the doc's name?


	7. July 12th

I have noticed at least three stories and one fan video that all have the same basic premise. This is one of the stories. I believe we all just came up with the same idea. Great minds think alike. I wonder if season 5 will run along the same lines.

 **oO0Oo**  
 **July 12th**  
 **oO0Oo**

Jolted into action, Finch moved to the passenger side door. "Get in. I will direct you." Knowing they would need the light from the car's headlights, he directed Sievert to where Root continued to work over John.

The car bumped over the curb and drove as close to the small group on the shore as possible. The doctor parked the car where the headlights would provide the best illumination, got out, grabbed a large bag from the back seat and hurried over to John.

Shaw had dragged herself over as well, and was doing her best to assist. Both women accepted the doctor's presence without comment. Both were too desperate and tired to do anything else.

Finch stared, wide-eyed and wondered at the doctor's presence. Had the Machine sent him? It must have. But how? Who was this man? Why was he helping them - no questions asked?

Eventually Root sat back on her heels and watched as Shaw assisted the doctor in stabilizing John.

Finally, after what felt like an eternity, Finch saw the doctor say something to Root who stood and made her way towards him. "It's not as bad as we feared. John had a vest on. He was shot from too close for it to stop the bullet completely, but it slowed it down enough to save his life. Your friend there says John will be ready to move soon and we should try to find something we can use for a stretcher." Root shot the doctor a look. "Where'd he come from, anyway?"

Finch wasn't really listening to her, though because he suddenly remembered seeing an old cot in the shack he'd explored earlier. He turned and began limping in that direction.

Root followed. "Harold?"

Without slowing or turning he answered. "I have no idea. He said he got a text. Could the Machine have sent it?"

Root scowled. "I guess we better hope so."

"A ringing payphone led me to meet him…"

But then they were entering the shack. Finch went straight to the old cot and gestured. "Will this do?"

Root smiled a small smile and ran her hands over it quickly, checking to make sure it wouldn't fall apart just when they needed it most. "This is perfect. Let's go."

oO0Oo

Finally the ragged group reached the subway where they scrambled to set up something of a sick room. Under their carefully crafted cover identities, they had mostly been able to use typical medical services when they'd needed them. There had only been a few exceptions, so both Root and Shaw were surprised to see how much medical equipment Finch had managed to squirrel away.

Trying to ignore their questioning looks as he set up a pulse oximeter next to the defibrillator, Finch simply murmured, "Only the paranoid survive…"

Root and Shaw exchanged looks, and then shrugs, and continued to assist the doctor.

It was a good thing they had because suddenly Dr. Sievert said, "He's crashing!" He looked to Finch with a rather desperate look on his face. "What meds do you have here? I need epinephrine - adrenaline?!" He turned to Shaw. "Prep the defibrillator!"

Finch moved as quickly as he could to a case filled with medicines. He brought it over and Sievert pawed through it quickly, grabbing the appropriate bottle and preparing a syringe.

"Uh… Doc?" Shaw spoke from where she stood on the other side of John, watching the monitoring equipment. "He's stable."

Sievert paused and looked. Then he put the unopened bottle away and disposed of the syringe. Frowning, he resumed his efforts.

Eventually he straightened, turned, took a deep breath and addressed them. "Reese is stable for the moment." He was not surprised to see three shocked looks at his use of John's name. "I know you don't know who I am. And I know you have no reason to trust me. But you must believe that I am here simply to try to save this man's life. He is not out of the woods yet. We very nearly lost him twice, only to have him somehow rally... He's a fighter.  
Our next step has to be getting that bullet out of his chest. It's not deep, but with the complications from his near drowning, we will have to be careful.  
Miss Shaw will assist me. Mr. Finch, you will monitor John's condition and provide us with any supplies. Miss Groves, I suggest you keep your gun pointed at me at all times since no one here should be comfortable with me holding John's life in my hands."  
He looked across at Shaw. "If you see me do anything that would harm John. Tell her to shoot me." Glancing around at the three he asked, "Everyone comfortable with the arrangement?" When there was no response, he finished, "Then let us begin."

oO0Oo

Many hours later, three exhausted people sat near John's unconscious form. Shaw had, at Root's insistence, and Finch's encouragement, gone to lie down for a few hours. She was more drained than any of them.

Root continued to half-heartedly point her pistol at the doctor who sat with his head back against the wall and his eyes closed. He seemed to understand that he was at their mercy. "How's your arm, Harold?" She asked softly, stifling a yawn.

They had managed to bandage each other's wounds while Shaw and the Doctor had worked on John. Both of them would need further attention, but as the wounds were far from life-threatening, both felt they could wait.

"It's fine." Harold answered. "I don't think it will need stitches. You on the other hand…"

"Sameen can look at it when she wakes up." Root answered dismissively.

"You should both have some antibiotics." Sievert spoke without opening his eyes. "Soaking an open wound in the East river isn't the best way to avoid infection." He raised one eyebrow in question and looked over at them. "If you trust me, I can prescribe something."

But Finch had already hauled himself to his feet and was crossing the room to the case of meds he'd opened earlier. "No need. Antibiotics are one thing I have become quite familiar with over the years." He handed Root some pills and a bottle of water. He also took some for himself and returned to his seat where he could observe John. "Is he going to be okay, Doctor?"

Root frowned at the question because she was of the opinion that they should be questioning the doc about other things - like where on earth did he come from? - but she waited.

Sievert closed his eyes and lay his head back once again. "I think so. As I mentioned, he's gone over the precipice more than once while in my... care, only to stabilize once again. You saw it happen. I've never seen anything like that before. Quite frankly, it's not normal. It's not even human. I can't imagine how he's doing it. It's almost as if…"

"It's almost as if he was getting an injection of adrenaline each time." Shaw stood leaning against the door jamb. She was bleary-eyed and obviously in need of more sleep, but they all were. And none of them were going to get it until they had some answers - until they knew John was going to live.

Shaw moved towards John as she directed the doctor. "Check his right shoulder. It's his most recent wound."

The doctor stood wearily and moved to do as she asked. Finch and Root just frowned, puzzled.

Shaw explained as she watched Sievert. "I couldn't sleep, so I was thinking about what our mysterious doc here just described. He's right. It's exactly as if John were getting an automatic injection of a powerful stimulant every time he nearly dies. That shouldn't be possible - unless…"

Sievert was examining the mostly healed scar on John's shoulder, a souvenir from his time up north. "You're right. This was recently, surgically opened. It's skillful work - barely detectable unless you know what you're looking for." He looked up at the group, hoping for an explanation, but even if they'd had one, they weren't about to share it with him.

Instead, they looked at each other. FInally, Finch took charge and spoke to the two women. "Unlike at the library, I have nowhere to detain him securely while we investigate. But there are far too many questions, and while I'm sure Mr. Reese could answer most of them, I fear he may not be able to for some time.  
I do not trust the doctor any more than either of you, but he has done nothing but help us so far. I suggest that we restrain him here, near John, where he can continue to monitor his condition, while we conduct our own investigations."

Shaw nodded. "I'll lock him up."

"Please be certain that he is able to rest as well. We may yet need him to assist in John's care."

She grimaced, but went to do as Finch had said. The doctor meekly put out his wrist for the cuffs. He'd expected a lot worse.

When she was finished, they gathered in another part of the subway, out of earshot of the doctor.

Root grimaced and sat down dejectedly.

""Miss Groves?" Finch asked in concern.

She looked up at him. "I'm glad John's okay. But… I can't help thinking that all of this is over. We can't possibly continue helping the numbers now. Our cover identities are ruined."

Finch consoled her. "We cannot know that for certain - it's simply too soon. We must continue to gather facts."

Root gazed back at him for a long while. Finally she sighed. "Okay. Then the first question is.. Who IS this guy? Where did he come from? How did he know we needed help?"

Finch shook his head helplessly. "He said he received a text telling him to be there. I assumed it came from the machine. I have no other explanation. As to his identity, I will research that immediately."

Shaw added, "What about John? I have a theory, but I'd need some sort of imaging equipment to test it since I really don't think he should go through another surgery right now. I don't suppose you have an X-ray machine?" She challenged Finch.

Finch stared at her. "You think something was implanted? Inside him?" He asked incredulously.

She shrugged. "It's possible. Unlikely - but possible. And it would explain some things."

He shook his head. "I have a small portable ultrasound. Would that do?"

Shaw nodded. "It should."

Root concluded. "Sounds like we have our first steps. We need to get this figured out fast. For all we know, the good doctor could be a spy for Samaritan, and we led him right here!"

"Oh please!" Shaw protested. "Do you think I would have let him anywhere near this place without making sure he didn't have a tracker on him? And if it turns out he's not on our side…"

Finch looked at her with concern.

She shrugged. "He won't be leaving here alive."

 **oO0Oo**  
 **TBC...**  
 **oO0Oo**

Please leave a note and let me know what you think.


	8. July 13-14th

A/N - oh no! It's the dreaded 'exposition chapter' hang on and bear with me…

I seriously considered separating this into two stories. The first would end here and then the battle with Samaritan would be a sequel, but I just couldn't find a way to close one story without starting the next. But we are gathering ourselves for some more excitement!

Thanks for coming along!

 **oO0Oo  
July 13-14th  
oO0Oo**

Shaw had just finished rebandaging the graze on Finch's arm. It had been difficult since the man wouldn't stop typing. But it could have been a lot worse. She was still amazed at John's marksmanship - not that she would ever tell him. Even in the intensity of that moment - he had managed to hit both Root and Finch with enough force to send them over the bridge railing, but had done no real damage to bone or muscle. Not an easy feat.

Now she was itching to get at that ultrasound to test her theory, but Finch had begged her to give John a few more minutes rest before he was disturbed. His condition remained stable for the moment, but he'd been shot, and nearly drowned, and no one really knew what had happened to him during his months with Samaritan. His condition was precarious at best.

Before she could say anything about it, Finch stilled. Shaw had come to recognize that sudden lack of movement. It meant he'd just discovered something big. "Finch?"

He glanced over his shoulder to where Root sat half-heartedly guarding the doctor, and spoke softly. "Dr. Michael Sievert was one of the top trauma surgeons in Boston for several years." He stopped, but Shaw knew his silence was pregnant and waited. "He left the hospital to work for a cutting edge company… called… Decima Technologies." Then Finch turned and looked up at her with fear in his eyes. "Our good doctor works for Samaritan."

Shaw didn't spare a moment. Her features went dark, she pulled her weapon, strode over the doctor and pressed it to his temple. Hard. She didn't say a word.

"Okay! Okay!" Sievert put up his hands as much as the cuffs would allow and ducked his head. "I knew it was a risk not telling you. I wanted John to be able to explain. I knew you'd listen to him. You have no reason to believe me, but there is a LOT more going on here than you know. PLEASE!"

Root had backed away a step at Shaw's sudden approach but now she stepped forward and laid a gentle hand on her shoulder. "Maybe we should at least hear him out."

Without taking her eyes off her prisoner Shaw asked Root, "He works for Samaritan, Root. Is _your machine_ telling me to back off?"

Root grimaced. "She hasn't spoken to me in weeks except to tell me to meet you by the bridge. That is the only thing I've heard. Anything she says to me, Samaritan hears as well."

Shaw grimaced. It was obvious how much she wanted to pull that trigger.

Sievert had gone silent, knowing anything he said would only harm his cause.

Finch's gentle voice joined in. "I would at least like to hear what he has to say."

Shaw stared at Finch. She nearly growled. "Do you know what this means? HE'S the one who _tortured_ John." She turned back to the doctor. "Aren't you?" She pressed the barrel harder against his head. " _Aren't you?_! Finch? Do you have _ANY idea_ what this man did to John?"

"I'm sure he's not the only doctor Samaritan employs - how can you be certain-"

"No!" Shaw shouted and cocked her pistol.

"She's right." Sievert murmured, defeated.

Shaw's finger tightened on the trigger.

John gasped. A sudden, deep inhale that drew everyone's attention.

oOo

Suddenly the room went utterly still except for the monitors around John. Several lights began to flash, indicating he was in some kind of distress. Four pairs of eyes were riveted on the form in the bed.

"Finch?" Came a barely audible whisper.

With one last glance at Shaw to make sure she wasn't going to do anything - yet - Finch hurried to John's side. "Mr. Reese? Are you alright? How do you feel?" Because he was pretty certain there was no way John should be awake just yet.

John ignored the question. "Did it work?" He murmured, still short of breath. "Are you okay?"

Finch leaned over the barely conscious man and placed a gentle hand on his shoulder. "Yes, Mr. Reese. You saved us all." He murmured. He still had no idea what was going on and he wasn't sure if John would be able to explain.

John's eyes became unfocused as if he was listening, or thinking. Then he raised his eyes to meet Finch's. "Don't shoot him... He's on our side… " Then there was another pause. "Root." He managed to gasp out.

Finch frowned for a moment before understanding that John was requesting her presence. He looked up. "Ms. Groves?" Then he stepped to the side as Root approached.

Shaw kept her pistol pointed at the doctor's head, safety off, ready to fire. She didn't take her eyes off him.

When Root came to stand next to the bed, John's eyes slid shut. He fought to open them. "Again." He whispered.

"No!" Sievert risked Shaw's wrath with that one word of protest.

"You must." John whispered. Then suddenly, he sucked in a lungful of air, his back arching slightly off the bed. He blinked rapidly.

Several alarms began to beep.

The doctor started to rise but thought better of it when Shaw moved to take an even more threatening stance.

"John?" Root asked in concern.

When he managed to catch his breath, his eyes locked on hers, and he began to recite a long alpha-numeric code.

Both Finch and Root understood what he was doing simultaneously. Finch grabbed a pen and pad of paper off the desk and handed it to her. She began furiously scribbling what John was saying.

Finally he stopped, gasping, and said, "Update." His head fell back onto the pillow as Finch hurried once more to his side.

John looked wearily over at him. "They'll explain…." A slow blink. "I'm… Sorry…"

"Don't give it a thought, Mr. Reese. You did what you had to to save our lives. Nearly giving your own in the process." Finch fought to reassure him before he lost consciousness. "Rest. John. Heal." He lay his hand once again on his friend's shoulder, not knowing if the man heard him or not.

John was once more unconscious.

oOo

With a last backward glance at Finch, Root went straight to the computer that would allow her to update her cochlear implant.

Finch turned to Shaw. "John said he was to be trusted."

"Yeah!" Shaw snorted incredulously, "John wants us to _protect_ the guy who _brainwashed_ him.. Doesn't anyone see how ridiculous that is?!"

Finch turned to the doctor. "Perhaps it would be best if you did try to explain."

Glancing warily at Shaw, he began. "You're right. I tried to brainwash him.. I even… got permission to use our more… intense… methods because he was resisting." His voice dropped to a whisper. "I thought what I was doing was right."

"You thought wrong." Shaw commented drily.

"I know that, now." Sievert responded quietly, and shook his head. "No matter what I did - no matter how brutal I was… John was patient. He was calm - quiet. He forgave me. He kept forgiving me. Then he started telling me things about myself - things from my childhood that he couldn't possibly know. Long-forgotten things my Grandmother had taught me - about grace - about forgiveness and second chances. About redemption." He breathed a long shuddering sigh. "I was supposed to be changing the way he thought. Instead he changed me."

Shaw relaxed a tiny bit. Finch saw it and was able to breathe once more.

Sievert continued. "Once I… understood what Samaritan really was, I began helping John any way I could. I was so afraid at first - I didn't do much. I didn't do enough. But he had a plan. He knew what he was doing from the very beginning. He had two objectives and he was very focussed."

"What were his objectives?" Finch asked.

"Most important to him was all of you. He knew he had to make them believe you were dead. Since they had seen through his cover, they kept getting closer and closer to finding you. That was his priority." He looked up at Root as she approached, smiling. "His second objective was uploading something into Samaritan. He had the entire program memorized..."

"Well… not exactly memorized…" She smiled.

She looked more radiant than Finch had seen her in weeks - and he knew what that meant. "The machine is talking to you again."

"Yes!" Root crowed, positively beaming. "And she has a lot to say. I told you she has a plan, Harold. We just have to trust her."

Finch frowned and gestured toward John's unconscious form. "THIS is the machine's plan?"

Root just smiled. "The Big Lug is right. The doctor is on our side. In fact, you can un-cuff him. He'll keep an eye on John. I have things to do!" She grinned again, nearly bouncing towards the door. "Shaw? I need your help."

When Shaw rolled her eyes and looked as if she had no intention of following, Root became a bit more serious. "John will be fine. She's looking after him. And…" She couldn't help grinning again. "We might just have a chance of defeating Samaritan after all... I need your help, Shaw!"

"Are you crazy?" Shaw asked. "Wait - strike that…" She shook her head. "We still have no proof that this guy is who he says he is. Are you just going to buy his story?"

Root tilted her head. "Actually, we do have proof. _She_ says he's telling the truth. He was John's target all along. She knew he would be the most likely person in Samaritan's employ to help. She told John, and he… got himself in contact with the good doctor. Then she told him all that stuff about Grandma, so Sievert would listen. So yes, Sameen, we have proof. Now can we go?"

Shaw sighed. How did she get herself mixed up with these people? With one last look and Finch and John, she followed.

oO0Oo

In the morning, Finch was still sitting, keeping watch over John. With both women gone, he did not feel comfortable leaving.

Dr. Sievert had laid down on the bench and was dozing when John began to stir. Finch immediately sat up. "John?"

John smiled a little, wearily. "I'm okay, Finch. Are you sure you are?"

"Yes, Mr. Reese. You succeeded in your mission with a minimum of damage to any of us." He paused as John watched him from under heavy lidded eyes. "Can you explain what has happened over the last couple months?"

"I'm sorry to have kept it all from you, Finch, but it was for your own safety. No one could know."

"Know what, Mr. Reese?"

"Your machine's plan. Actually, apparently it was originally _your_ plan… some kind of Trojan Horse?" John settled himself a bit more comfortably although he did not miss Finch's slightly widened eyes at the mention of his Trojan Horse. John began to explain softly. "I was approached completely out of the blue a week before I disappeared by Dr. Tillman. She said she'd started using a dating site, but her first date wasn't what she'd expected. A man came to meet her. He gave her a package, but he didn't know what was in it. It contained a letter for me, and a medical device something like a small defibrillator."

"So you do have an implant?" Finch asked incredulously.

John nodded. "It's similar to a pacemaker, only far more powerful, and it has a reservoir of adrenaline." He didn't explain why. He didn't need to.

Finch cringed.

"Unlike a pacemaker, it's completely internal and undetectable without some equipment. It also has the ability to vibrate in patterns. That's how the machine was able to communicate with me without being detected by Samaritan: antiquated broadcasting systems and Morse code."

Finch felt quite strongly that John was missing the point. "But you were tortured."

John just blinked slowly. "I had to infiltrate Samaritan and there was no other way. With the doctor's help," who continued to snore nearby, "I was ultimately able to convince Greer that you're all dead, and upload some software your machine needed."

At the mention of the software Finch's interest piqued. "Software? My Trojan Horse?"

"The machine told me that it was a way to create another blind spot - a vulnerability? A way for your machine to attack Samaritan."

Finch's eyes widened, and he stared, trying to take it all in. Finally he continued. "Well, now you can rest." At the moment, Finch wasn't at all certain his machine had anyone's best interests at heart.

But John shook his head. "Sorry, Finch. This is just the beginning."

Finch looked up at him, fearful of what he would say next.

"What I did only gave us a place to start - a thread to pull. We are not in a good place here, Finch. We've backed ourselves into a corner and now we have to fight our way out. Your machine thinks it can win - with your help." John regarded him for a moment. "I just hope it's right."

Finch frowned uncomfortably. "What is next?"

John shifted once more. "As I understand it - now you and Root have some work to do and Shaw and I get to make sure you can do it. But ultimately the machine made it very clear to me that this is its fight, not ours."

"What does that mean?"

"If everything goes as planned, your machine will merge with Samaritan and fight it on a… I don't know…" he searched for an appropriate word. "a 'cellular' level - one line of code at a time. What will emerge at the end will be a new machine - but hopefully - one with all of _your_ parameters in place."

Finch sat down heavily. He was staggered by the audacity of the plan. The idea that his machine would go to war to protect him - to protect humanity was unbelieveable. And the worst part was, he was not confident that his Machine could win. "Samaritan is so powerful." He whispered.

John nodded. "Your machine says not to worry, that much has changed since you set it free."

Finch's mind was buzzing with the possibilities. This was something he's never considered - could barely grasp. But now, as he thought about it, he could see possibilities. He was becoming more and more intrigued. "The machine that emerges will be even more powerful that either machine on it's own…"

John sat up and swung his legs over the side of the bed.

"John!" Finch protested.

But John was done lying in bed. "I'm fine, Finch. The vest kept the bullet from doing any real damage. It's barely more than a bruise."

"You had surgery!"

Dr. Sievert had been woken by the commotion and sat up yawning. "I had to remove the bullet - but John's right. It wasn't deep. As long as he doesn't develop pneumonia or get an infection at the site, he'll be almost back to normal in a few days."

Finch plopped back into his seat. He supposed he should be used to Mr. Reese's near-miraculous recoveries by now.

oO0Oo

At that moment, Root and Shawn returned. Shaw looked a little annoyed, but Root was absolutely buzzing with excitement. Thanks to the code John had given her, the machine was able to communicate with her freely for the first time in forever and she was on top of the world.

"Did John tell you?" She chirped to Finch. "Isn't it exciting?!"

Finch raised his eyebrows and looked back and forth between the teammates. If the Machine was taking these kinds of risks, then John was right- one way or another, this was the beginning of the end.

Shaw rolled her eyes, John looked a little bemused, Root simply beamed and continued without taking a breath.

"We have so much planning to do, Harry! And John and Shaw have their own work to do. Let's get busy, shall we?"

Root herded Finch into the rail car and the bank of computers as Shaw sauntered over to where John sat on the side of the bed.

"You sure you're up for this?" She asked out of the corner of her mouth. "You were pretty much dead a few hours ago..."

John just looked at her.

She smirked. "Then let's go."

She stepped to the side as John eased himself off the bed and went to get dressed.

 **oO0Oo  
TBC  
oO0Oo**


	9. July 21st

Special Thanks and Virtual Cookies to: ElliQuinn, elaine0510, Lady Sundiver, poi922, fanfictionfan63, M_E_ Lover, IrrelavantSherlock512, dancing_dog, Lucky7, sandunder, Aussie_Muggle, Dragonesse, mizwidget, TVjunkie, Madoshi, Aussie_Muggle, Fandom_Person_of_Interest_2015 (Fandom_Person_of_Interest_2014), allapplesfall, and LeggoMyEggoMeggo, and all the guests who left comments and Kudos. These stories would not exist without you!

 **oO0Oo  
July 21st  
oO0Oo**

A week passed where Root and Finch barely left the rail car, John and Shaw were rarely seen, and Dr. Sievert tried to keep himself occupied and out of the way. He'd tried to leave, but the moment he did, Root had popped her head out of the rail car and informed him with a smile that _'She_ wasn't finished with him yet…' and he should 'have something from the vending Machine.'

John and Shaw were often gone for days at a time. When they did show up, it was always in the early morning hours and they were always dressed in full black with either masks or dark smudges on their faces. They were doing extensive surveillance on one of Samaritan's hubs - the one the Machine had informed John would be most conducive to their success. Harold just hoped John was getting some recovery time.

On one of their rides home, Shaw had remarked to John that they _could_ involve Fusco in their efforts. It would be nice to have a little more manpower. The poor detective was still operating under the impression that John was MIA. Since they'd stopped communicating with him in order to work on their new objective, it must have seemed to the detective that they all were. He'd contacted her to see why they had all seemingly fallen off the face of the earth. She, of course, hadn't told him anything.

But John was adamant. "Keep him out of this. He's safer where he is, and we may need him most when this is all over… one way or the other."

"You don't think we're going to win." Shaw commented flatly.

"Shaw-" John responded calmly, his eyes on the road, "You know as well as I do that it doesn't help to predict an outcome. Work toward your objective and adjust tactics as needed. We'll get Finch and Root in there. And we'll protect them for as long as we can. Beyond that - we'll just have to wait and see."

Shaw had scowled, but hadn't responded. She knew John was right and it irked her that he seemed (at least on the outside) to be even less emotional about what they were about to attempt than she.

"By the way," John said. "Thanks for taking that punch for Finch."

Shaw smirked. "Well - I did get to shoot you once, so I guess this makes us even."

John's eyebrow twitched. If anyone was seriously keeping score, a single shot from a small caliber pistol and one punch to the nose was hardly equal to several bullets from a fully automatic machine gun. But who was counting?

Shawn changed the subject before he could comment. "You took out that sniper that had me in his sights, didn't you?"

John didn't respond at first but gave a tiny smirk. Then he relented. "Samaritan thought I was the guy's back-up."

Shaw shook her head. "You backed him up, all right."

oO0Oo

Finch and Root continued to write code.

While John and Shaw were able to find some enjoyment in their activities, the pair in the subway could only feel the ominous cloud over their heads.

They were doing everything possible to arm the Machine for it's upcoming battle. They also spent a considerable amount of time debating the Machine and the nature of it's programming. Finch still wasn't convinced the Machine was as benevolent as Root insisted, but he sincerely hoped she was right.

Finch did most of the writing. His main priority was to do everything possible to reinforce the moral code he'd imbedded deeply into the Machine's programming.

Root mostly contributed with comments and direction from the Machine. Her main priority was to make the Machine powerful and ruthless enough to win.

Neither one knew if their unique combination would be enough to make them victorious.

Both of them knew that if the Machine won, but lost the special qualities given to it by it's creator, it would be a very empty victory.

They would only have created a new, even more powerful enemy. And they would have lost something exceedingly precious to each of them, if for different reasons.

oO0Oo

Fusco worried. Not only had his friends vanished, but something strange was going on. Positions of power kept changing hands. Policies, rules, and laws were changing almost too fast for him to keep up. There was just something off. He didn't understand what it was, but he didn't like it.

Samaritan and Greer, thinking their enemies were vanquished, had begun the push to take over the world.

The Machine knew this and exhorted its assets to work faster.

Finally - they were as ready as they could be.

oO0Oo

There was a somber but anticipatory tone in the subway as the four friends gathered one last time before setting out on their mission. They were dressed in all black, and each person had a balaclava folded up on top of their heads, ready to be pulled down to cover their faces. Finch looked uncomfortable in his unusual attire, but John had assured him that it was absolutely necessary, and had admonished him to remove his glasses at the appropriate times so they wouldn't catch the light and alert Samaritan to their presence.

They all stood silently for a moment. Each of them knew they might never gather here together again - that there was a very good chance that one or all of them might not return.

Finally Finch spoke. "I've said this to each of you before… but none of you should feel obligated-"

John didn't let him finish and Shaw, by her rolling of eyes silently showed her agreement. His voice, when he spoke was soft, earnest and sincere. "Harold, you told me a long time ago exactly what was at stake. We all know." He gestured around at their little band of misfits. "We are all right where we need… where we _want_ to be." He looked at his friend. "I, for one, am right where I belong."

Shaw nodded solemnly behind him.

Finch regarded first John, and then Shaw and marvelled at the loyalty, the friendship he had neither sought, nor felt he deserved. And yet he was so immensely grateful, he had no words to express it. He looked back at John and knew he was understood anyway. "Thank-you." he whispered.

John nodded once and cleared his throat. "Getting _in_ will not be a problem. Shaw and I are quite familiar with the workings of the facility and we can get you into the control hub without being seen. Once you are there you will have to work as quickly as possible."

Shaw took over. "We have no way of knowing how long it will take them to detect you or how long it will take them to respond." She glanced sideways at John. "I wanted to mount a minor attack just to see how they responded but Captain Careful here said it was too much of a risk."

John did not respond to the needling. "We cannot give Samaritan any reason to watch this location any more closely than any of the others. Shaw and I will keep the enemy away as long as possible but you will have a limited time frame."

"We shall endeavor to hurry." Finch murmured in response.

"What about getting out?" Root asked.

John just grimaced and shook his head once.

Shaw answered her with a shrug. "By the time you're ready to go, Reese and I should have a… _really…_ good idea of what their defences are capable of and we will… adjust accordingly." She finished, using one of John's intentionally vague phrases.

Root gave her a small smile. "Well, we best be going then. It'll be dark in a couple hours."

They filed out, Shaw leading the way. John followed, a heavy looking black duffle bag slung over one shoulder. Root paused and waited for Finch who had stopped to give one last look at their haven. He had the distinct feeling he would not return, but if they were successful, it would be more than worth his life - all their lives.

oO0Oo

Two hours later they were all lying on the ground at the crest of a hill overlooking the facility. The non-descript box of a building was fairly well lit and two guards with dogs patrolled the perimeter.

Shaw glanced at her watch and grinned at Reese who ignored her and continued to watch purposefully. The exchange was not lost on Root who smiled as well and asked playfully, "What have you two got planned?"

Then John's eyes narrowed briefly in satisfaction as the one visible guard wrapped an arm around his middle and began to stride quickly towards the entrance.

Shaw just grinned at Root who raised her eyebrows, clearly impressed. John slid smoothly into a crouch and started silently down the hill with his black bag of tricks.

Shaw slid into his spot next to Finch. "When John reaches the fenceline, we go." She whispered.

A moment later they all did their best to mimic John's movements. When they reached him he had a hole in the fence ready for them to crawl through. Finch glanced at the wiring John had put in place and realized that the breach would remain undetected.

Once they were through, Shaw led them to the door. John stayed behind long enough to shift the cut fence so that the gap was virtually undetectable, then followed.

Once he reached the small group, Shaw nodded at him and entered, gun drawn and held at eye level. Finch and Root followed, imitating their teammates' silent movement. As they moved, they could hear the dogs barking, and the two guards moaning behind the bathroom door. It was hoped that the guards would chalk the dog's anxiety up to their own discomfort. And so far it appeared to be working. Shaw reached over and quietly slipped the lock on the door.

She had explained on the drive over that the interior of the building was only minimally guarded. There were, however, cameras everywhere, allowing Samaritan to guard itself. She and John had managed to get in and out undetected several times over the last days. Each time one of them entered, they shifted one of the cameras ever so slightly away from its prime view. Once the first camera had been shifted enough to allow them to pass unseen, they moved on to the next. Slowly they had created a very narrow but invisible path from the entrance to the control room. As far as they could tell, Samaritan hadn't noticed.

It had been incredibly tedious work, and as he saw what they had done, Finch couldn't help but be impressed with the amount of patience required. He suspected it hadn't been an easy thing for John to keep Shaw motivated to be more scalpel than hammer. Now it was hammer time, and he could feel the excitement and anticipation flowing off of her. Personally, he felt mostly fear.

Of course, the possibility remained that Samaritan had been aware all along and was just waiting to trap them. Both John and Shaw knew this but neither felt the need to mention it. It wouldn't change a thing.

The only other guard was inside the control room. He watched cameras and monitored the temperature and general functions of the building. All of his attention was on the banks of monitors and computer readouts in front of him so he was taken completely unaware by Shaw's choke hold, which she followed up with an injection that would ensure his silence for several hours.

Finch merely raised an eyebrow at John who responded with a slight shrug. "Told you getting in would not be the problem."

Finch wanted to ask questions, but he didn't have time. Root was already opening their own case and plugging cords into the appropriate outlets. "It won't be long before Samaritan realizes what we're doing…" She glanced behind her and realized that Shawn and John had already left. She rejoined Harold in their efforts to essentially re-program Samaritan.

The program that the Machine had earlier uploaded into Samaritan via John during his incarceration had been very quiet. It had been such a small change that Samaritan had merely accepted it. But it had created a tiny 'crack' in Samaritan's programming, and now Finch and Root would take advantage of that crack to 'let the Machine in.' The two of them began typing furiously.

John and Shaw dug into his bag of tricks and split up, still staying out of sight of the cameras. They got busy setting different traps, small bombs, smoke grenades, and incendiary devices all throughout the complex. Anything that could possibly aid in their escape. All four of them already carried gas masks in preparation. It was very difficult to shoot someone through a cloud of smoke, and neither side would have anything but the slightest help from the supercomputers as the AIs would be engaged in a battle of their own.

It was only seconds after Finch and Root began that they were detected. Alarms began to blare. Lights began to flash. The two guards in the bathroom began trying to break down their locked door. Reese and Shaw glanced at each other and then made their separate ways to their predetermined look out points. Both were heavily armed and carrying plenty of extra ammo for each of their weapons. Both had the building memorized. They knew the primary objective was to allow Finch and Root to finish. The secondary objective was to get the two of them out alive. Their own escape was a distant third, and neither one saw any problem with that.

Now all they had to do was wait for Samaritan's cavalry to arrive. It wouldn't be long.

The one thing they hadn't planned on was Samaritan's ability to defend itself. While Finch and Root worked in the control room and Reese and Shaw watched entrances, suddenly the fire suppression systems turned on. Air was quickly being sucked from the building. Finch had known of the possibility of this tactic and had hoped that the effects would be confined to the clean rooms where the drives were actually stored. But that was not the case. Thankfully, he had insisted that their gas masks would double as oxygen masks and be equipped with small air tanks.

All four of them donned the masks and returned to their assignments. Only Finch gave a thought for the two guards, although they all felt regret for the dogs. If anyone still needed evidence that Samaritan was pure evil, that was it.

Soon there were emergency lights flashing outside the doors as cars and vans full of Samaritan's heavily armed sycophants arrived. John shifted position, took a deep breath and armed his weapon. Shaw unknowingly mirrored his movements from her position guarding the other entrance.

She then murmured into her comm to let the Finch and Root know the 'party' was about to begin in earnest.

"Here we go."

oO0Oo  
TBC…  
oO0Oo


	10. July 21st con't

**oO0Oo  
July 21st con't  
oO0Oo**

The storm of bullets began but Reese and Shaw had chosen their positions well. Samaritan's lackeys couldn't advance without walking directly into their line of fire. No one succeeded in entering the building until someone tossed a grenade in Reese's direction. He was forced back, thankful he'd kept his mask on.

Shaw was facing her own obstacles. It took a little longer, but the operatives outside finally came up with the grenade idea as well.

Their enemies were hindered by the need to keep the building intact in order to protect Samaritan. Reese and Shaw had no such qualms and set off the first of their bombs almost simultaneously.

The explosions gave them time to retreat to their next carefully chosen positions. Their plan was to hold off both forces as long as they possibly could, carefully herding their enemies exactly where they wanted them. Eventually they would join forces near the control room where their primary activity would change from protection to exfil. They had a potential escape route planned, but no real way of ensuring it would be clear when they needed it.

"How's it going in there, Finch?" Reese inquired somewhat breathlessly. Root answered for him. "We're nearly half done. Samaritan is-" a burst of static interrupted her. "Fighting back." She finished and Reese could hear that they were dealing with their own kind of chaos.

Shaw and Reese met as they'd planned. Unfortunately it was much more quickly than they'd hoped. At least by this time, their carefully placed traps had sent the enemy into disarray. The somewhat organised firefight had digressed into occasional hand to hand as well as an exchange of bullets, knives, and in one case, a chair. Then Shaw found herself faced with an extra-large opponent. She wondered briefly where these guys came from and why they never seemed to join the good guys, before throwing a completely ineffectual punch at the man's nose.

This was not good. Root and Finch needed several minutes yet - if this guy took her out it would open a wide path directly to the control center, leaving her teammates' backs exposed. If she didn't take this guy out, their mission was finished.

Although she would never admit to being thankful for the help, she did not protest when Reese appeared over the guy's shoulder and grabbed him in a choke hold. The guy managed to get a hand in to protect his airway,though and Shaw knew he would not go down easily. She threw a couple dirty punches that might as well have been feathers. He countered with a wild punch that just glanced her jaw but was still forceful enough to send her flying. Then the guy flipped John and they began to wrestle.

Shaw was torn between the need to help Reese and their mandate to keep the enemies away from the control room. But to keep Finch and Root safe she needed Reese and she needed to get this neanderthal out of the way - not to mention that, at least at the moment, it looked like John was losing. She grabbed a piece of table that had broken under their combined weight, waited for an opening, and cracked it over the guy's skull. It barely dazed him.

Then John gasped to her as he twisted to get a better grip. "Shaw... clear." She frowned for a moment, but when he repeated "CLEAR!" more forcefully she understood. John still had that freaky implant. It hadn't occurred to her that it could be used as a weapon. Could the Machine even hear him at this point?

"No!" She cried. That kind of charge would certainly stop the behemoth, but it would just as certainly stop John.

"Get 'em out." John told her, making direct, meaningful eye contact for a moment. Then he cried "Now!" and Shaw knew he was no longer talking to her. He was asking the Machine to make serious use of his implant. There was a barely audible hum of electricity and both men went perfectly still for a second before collapsing bonelessly to the ground.

Shaw watched for a split second longer to see if Reese would miraculously leap to his feet to continue the fight. She couldn't spare longer than that because the bullets began to fly from a new source at just that moment and she had to accept that Reese would never get up again. With no time to think about it, she did as she was trained, noting once again that being a sociopath could be handy when one of your best friends had just been killed.

She turned and ran. "You guys better be done." She shouted. "We are _out of time_."

"We'll be ready when you get here." Root shouted back. "For better or worse, we've done what we could." Then Shaw heard her shouting to Finch. "Harry! That's it! You've got to let her go. She can fight on her own from here… Harold…!" Shaw shook her head and finished her sprint just outside the control room.

Having studied the blueprints of the building, she and Reese had planned their escape route. A hallway that ran from the control room to a storage room appeared to be a dead end, but it ran along an exterior wall for about three feet. On the other side of that wall they had placed and hidden explosives that would blow a hole big enough to let them out of the building. From there all they had to do was clear the twenty feet to their hole in the fence, and make it back up the hill to where their get-away car waited - if it hadn't been discovered. "No problem." She mumbled to herself. "No problem at all."

Shaw rolled her eyes at the futility of it all and readied her weapon anyways. Their chances had been slim when they were all fighting together. Without Reese, she really didn't see how they could make it.

At least now, with her computer duties fulfilled, Root was able to join her. The woman was good with a weapon and Shaw was glad of the support. It seemed Samaritan's reinforcements had arrived.

"Finch!" Shaw shouted as she took down two more enemy agents. She was pretty sure that he'd probably stopped listening to Root a while ago. "We gotta go _now_ or we're not getting out of here." She continued shooting, Root beside her, bringing her own weapon to bear.

Finally she felt Finch behind her. "Where's John?" came the inevitable question.

She was tempted not to answer as she personally thought it was obvious, but she was afraid he wouldn't move unless she did. "He's on his way." She told him, but knew that her hesitation was enough to give away the lie. She felt him freeze and closed her eyes briefly, all fight had gone out of him. "Think about it later, Finch. John wants you out of here!" She told him harshly and began to back toward their escape, firing as she went. Herding Finch with her body, he had no choice but to move where she directed. Root's submachine gun was chattering away beside her. It was a good thing too, because she was finally out of ammo.

But at the same moment Shaw found herself unarmed, Samaritan appeared to be out of agents as well - at least temporarily. They had caught a break. Either Samaritan's goons had gotten smart and stopped throwing themselves into the line of fire, or they really were all down or dead. Shaw hoped for the latter and turned to warn Finch of the imminent explosion. Then she hit the detonator, thankful she'd insisted on carrying it instead of John and the hallway was filled with light and sound and flying debris.

Using the smoke as cover, she directed Root to lead the way and followed Finch.

Then they were out.

Shaw ripped off her gas mask and took a deep breath as she scanned the area. So far, unbelievably, it was clear. As they'd hoped, Samaritan hadn't anticipated their choice of escape routes. But it wouldn't last long. They needed to get through the fence as quickly as possible. The lane between the wall and the fence was far too well lit now that the emergency lighting had turned on. At least on the hill they'd have the cover of darkness - not to mention the back-up ammo she'd left there just in case.

Root was already halfway to the fence, but Finch just stood staring at the hole in the wall. She briefly closed her eyes because she understood what he was doing. He was waiting for John to appear. She approached and murmured in his ear. "I'm sorry, Harold. I don't think he's coming." She saw Finch twitch as if in pain.

"We have to go back. He would go back for one of us…"

Shaw continued more urgently. "We knew the risks going in. John did what he had to do in order to get us all out of here. If you don't move, we will ALL be caught because Root and I won't leave you here. Please, Harold. Don't let his sacrifice be for nothing. We can't go back for him, and you _know_ he wouldn't want you to. Please." She tugged gently on his arm.

Finally Harold turned his back on the building and moved silently, in a daze toward the fence where Root waited having reopened the gap for them.

Shaw caught herself staring at the hole a beat longer. But when John didn't magically appear, she turned and jogged after Finch. If they could get out into the dark before anyone saw them, they just _might_ have enough of a head start.

The look in Root's eyes as she stared over Shaw's shoulder told her things weren't going to be quite that easy. She spun on her heel raising her empty weapon reflexively as she did so.

Two of Samaritan's agents stood there with machine pistols already pointed straight at Finch and Root.

There was no time, and she had no ammo. They weren't going to make it. Especially since now a third figure was emerging through the smoke. She hoped the Machine could win on its own because its assets weren't going to survive.

But the third figure wasn't one of Samaritan's - it was John.

None of them could believe it.

Shaw, being closest, immediately saw that he was just barely staying upright. There was no way he could win a fight with two of Samaritan's finest in his condition - he had no weapon either. But she knew he would throw himself into the mix anyway. He would sacrifice himself so that the rest of them might be able to escape during the distraction. Samaritan would certainly finish him off.

"Not this time, John." She murmured and ran straight at the two men holding the guns. She vaguely heard Root shout her name. Her actions took all three men by surprise, but gave John a chance.

Root cried out when she realized what Sameen was going to do. She knew she should take advantage of the distraction to get Harold out of there, but she simply couldn't move. She couldn't take her eyes off Sameen in spite of the fact that she was sure she was about to watch her friend be killed.

The closest agent swung his pistol towards Shaw and shot off a spray of bullets, but his aim was off because at the same moment, John dropped a large piece of the broken wall on his head. Both Shaw and the agent went down hard. Furious and in anguish, Root let off a volley of her own at the remaining agent. By the time her vision cleared, John was already kneeling beside Shaw and taking her into his arms. He staggered to his feet and stumbled towards them.

Root wanted desperately to take Shaw herself, but Harold's hand was on her arm, his gaze imploring. So instead, she held the fence open wide and let first John with his precious burden and then Harold through. She reset the fence as she'd seen John do, making the breach once more nearly invisible in the gloom. Then she grabbed the spare ammo Shawn had hidden and covered their retreat.

More of Samaritan's lackey's poured from the hole in the wall and from around the front of the building, but it seemed the darkness was their friend. It wouldn't be long before they were spotted, but the car was now only feet away.

Then John fell. Root scrambled up to him. Finch was already on his other side, "Mr. Reese…"

"I've got her, John." Root interrupted as she pulled Sameen into her own arms. "Now get to the car." She told him. Finch pulled one of John's arms around his shoulders and together the four of them reached the crest, disappearing over it just as spotlights flooded the hillside.

Finch helped John into the front seat, then went around and helped Root get Shaw into the back before putting himself behind the wheel and peeling out in a spray of dirt and gravel. They were far from being out of danger.

"Miss Groves?" Finch inquired fearfully, "How is Miss Shaw?"

There was a pause before Root responded, a nervous thrill in her voice. "She's alive, Harry. We made it. We _all_ made it!"

Finch had thought John was out cold since he hadn't moved, but he whispered. "Vest caught the worst of it. She took one in the side. Hit her head when she went down. We're not out of this yet." As he spoke he dragged his phone from a pocket. The device seemed to weigh several pounds instead of a few ounces.

Finch knew it was pointless to inquire after his condition and so he concentrated on the road. Samaritan would soon be in pursuit.

"Hey… partner…" John was talking into his phone - apparently to Fusco. "I've heard you cops don't like it when someone messes with one of your own." He paused to listen. "Actually, it's good to hear your voice, too, Lionel," He said sincerely. "But we can do the reunion later. See - I could use some back-up… a lot... of back-up." And he gave succinct directions to their location. "I'll explain later." The rear window shattered. "Right now I'm a little busy -"

John reached down and grabbed a fresh machine gun. He dragged it first on to the seat and then up to rest on the back. Root had already pulled out its twin and they fired out the back window as Finch urged more speed from their vehicle.

Finally, after what felt like an eternity, there was a flood of lights and sirens from _in front_ of their car. Fusco had done his job well as the squad cars neatly parted to let them through and then closed ranks behind them. Without Samaritan's voice to guide them further, the enemy agents didn't put up much of a fight, their efforts now focussed on escape rather than capturing their prey.

They could ask Fusco how it all turned out later. At the moment, they were just glad to see the pair of ambulances he'd arranged to have waiting for them.

 **oO0Oo  
** **TBC…  
** **oO0Oo**


	11. July 22nd

A/N As of this posting 58 people have read the last chapter and only one person reviewed So M_E_Lover, this chapter is ALL for you! :-D You're awesome!

oO0Oo  
July 22nd  
oO0Oo

Harold Finch sat alone in a hospital waiting room trying to make sense of everything that had happened in the last twenty-four hours. But even more insistent was the question to which he so desperately needed an answer: _Had the Machine won?_ How long would it be before the answer became apparent?

The night before, in a maelstrom of flashing lights, sirens and gunfire, Miss Shaw and Mr. Reese had each been safely loaded into an ambulance. John had grabbed his arm and quietly told him not to let Shaw go to the regular hospital, but that he must. He also asked that Finch have Dr. Tillman meet him wherever he ended up.

That part, at least, made sense to Finch. John would not want to keep that implant any longer than absolutely necessary. While he was willing to use any tool imperative to accomplishing his mission - no matter how unpleasant - Finch knew he also saw no reason to keep it a moment longer than he had to.

Dr. Tillman had arrived shortly after John and had taken him into surgery as soon as Finch had worked his digital magic to get her privileges at this hospital. He hoped she would be out soon with an update.

He had called Dr. Sievert from John's ambulance, informing him that his skills would be required for Miss Shaw. And that he should prepare to once again perform surgery in the subway.

At the moment he'd been more worried about how Miss Groves would manage to get Miss Shaw from the ambulance into the subway without being seen. He was more than a little concerned about how the oblivious and innocent EMTs had fared. He didn't _think_ Miss Groves would merely dispose of them once they'd stopped being useful, but he couldn't quite be sure.

Now Finch really wanted to know how Miss Shaw was. He also really wanted to know what had happened to his more pugilistic teammates during their part of the mission. John had no outward evidence of an injury. What had happened to him? In that awful moment where Miss Shaw had informed him that John was dead he was certain she had believed it. Harold had assumed that John had been shot - or worse, but when he appeared he wasn't even bleeding.

The only thing Harold could think was that he'd somehow been killed, and the machine had used the implant and the adrenaline it contained to bring him back from the dead. No wonder he'd been utterly exhausted!

Harold also wondered what the regular police would make of the carnage they found?

At least he didn't have to wait long for an answer on that front. Detective Fusco appeared at the end of the hall and made his way to where Finch sat.

"You guys are crazy. You know that?" He asked a bit breathlessly.

"I admit, it does often appear that way." Finch responded quietly, "But we are all…" He paused, considering. "Nevermind. What can you tell me?"

"We found a ton of bodies-"

Finch interrupted, suddenly concerned. "How many wounded?"

Fusco just looked at him. "None - Don't tell me that surprises you…"

"As you know, detective, our methods are rarely fatal…"

"Humph." Fusco responded. "I don't know what to tell you… there weren't no survivors."

Finch raised his eyebrows and looked away, clearly disturbed by the news. He was certain that while John and Sameen may have been given no choice but to kill some, they would have avoided the use of deadly force as much as possible. Samaritan must have ended their lives to protect itself. Unless the AI battle was already over and the _Machine_ was responsible for the deaths of its enemies…

That possibility was very real and very disturbing. If the Machine had won, but lost its - for lack of a better word - morality - then all was lost and none of them would survive. Harold swallowed and unconsciously shrank back into his chair.

Fusco accepted the fact that he simply wasn't going to be read in on all the details of the operation - as usual. "Look. Is my partner gonna be okay, or what?"

At that moment, Dr. Tillman appeared at the end of the hall.

"Let's find out, shall we?" Finch said as he stood and went to meet her.

She looked warily at Fusco and chose her words carefully. "John's going to be fine. The surgery was successful. You need to be aware that there was some tissue damage to his heart. But nothing that won't heal over time. It's a good thing he's as healthy as he is.

He'll need some time to regain his strength, but with any luck there shouldn't be any lasting effects." She frowned at what she was about to say, but continued. "It would be good for him to stay in bed at least a solid forty-eight hours. In fact, I plan on keeping him sedated until tomorrow morning. But…" She grimaced, knowing a full forty-eight hours wasn't realistic for this man. "He can go home in the afternoon if he needs to."

Finch nodded his understanding and shook her hand. "Thank-you." He told her quietly and sincerely.

She nodded once more and left.

Fusco then turned to him. "That's good news. Nutella and Maybelline okay too?"

Finch offered a small smile in response. "Miss Groves was unharmed. I need to find out Miss Shaw's condition. However - her injuries did not appear to be life threatening" He pulled out his phone.

Fusco nodded, noticeably relieved. "Lemme know, kay? I gotta get back and make sure clean-up goes how it's supposed to."

Finch nodded as the detective departed and called Root.

"Hi Harry." Came a cheerful voice from the other end of the line. "Sameen's going to be fine. Dr. Sievert is just finishing up. The bullet went straight through and didn't hit anything vital. She's got a couple cracked ribs and a concussion, but she'll be fine."

Finch allowed himself the first deep breath he'd had in what felt like days. "And the EMTs?"

"Oh." Root chuckled. "I dropped them off and told them where they could find their ambulance later. It wasn't a problem."

Finch closed his eyes briefly, glad she couldn't see how relieved he was. Then he asked the question that weighed most heavily. "Have you heard from the Machine?"

There was a long pause. When Root spoke, her voice held none of its previous animation. "I haven't. I don't know what to think. We have no way of knowing how long this will take. It could, conceivably, take _years_ … The only good news is that we're all still alive. She hasn't turned on us and I consider that a _very_ good sign." She finished, a note of determination in her voice.

"Yes," Finch responded regretfully, wishing he could share her optimism. "They could still be fighting, or it could already be over. We will have to wait and see."

"We did what we could to help her, Harold. I _have_ to believe she will win."

"I wish I could share your confidence. The Machine is fighting against something more powerful and more ruthless than itself. We may yet lose."

Root made an attempt to sound hopeful. "She won't let you down." And she hung up.

oO0Oo

Twenty-four hours later, Finch was both more encouraged and more worried.

 _Encouraged_ because - against all odds, they were all still alive. Both John and Shaw were recovering and there was every reason to believe they would both be fine. He had to stop thinking about it. Every time he did, his eyes filled with tears and it was getting to be really embarrassing.

He was _worried_ because he still didn't know if the world had been saved or destroyed.

At the moment, he was waiting for John. His recovery was progressing as hoped and they would be heading back to the subway soon. Once there, he would make an attempt to determine the Machine's fate. Root had promised to wait… and watch.

If the Machine had lost - or had won but been irrevocably changed - no where would be safe for them - _especially_ not the subway.

Then John was standing next to him in his suit. They didn't speak.

Finch stood and led the way out to the car.

Both men remained silent on the ride home. There was nothing to say - and no reason to hope.

The light turned green and Finch proceeded to the next corner. He hadn't come to a complete stop before that light turned green as well.

John looked up at the signal thoughtfully. Finch frowned.

The next light turned green before they'd even begun to slow. So did the next - and the one after that.

Finally, John turned to look at Finch with a slight smile.

"Let's not get our hopes up yet, Mr. Reese." Finch murmured. "It might not mean anything at all."

John didn't respond. He continued to watch out the windows, but his smile was slightly more hopeful.

oO0Oo  
TBC...  
oO0Oo


	12. July 25th

A/N - started a new job so I have less time to work on this, but it's almost finished! Special thanks go out to everyone who reviewed and left kudos on this story! I appreciate you more than I can say.  
This chapter is dedicated to **adorestories** who actually left a prompt on one of my _other_ stories, "Outside Looking In" but I responded to that prompt here. I hope you like it, adorestories! It is also dedicated to **ElliQuinn** to pointed out an important issue I very nearly forgot to address. The last bit of excitement in this story is due to her efforts.  
Finally - I just want to say that many others have taken on the challenge of writing about the machine and what it went through in this war. I chose to focus on how it affected the human assets. (that's my favorite part about the show, anyway - the human interactions)

 **oO0Oo  
July 25th  
oO0Oo**

Their path had remained clear all the way back to the subway. But when the team was reunited, there was no further evidence of either machine.

For the next two days, things were very somber in the subway. Dr Sievert was finally allowed to go home with several warnings to be careful and stay out of sight.

Root and Shaw left occasionally on exploratory missions. Actually, Root left. Shaw wouldn't let her go alone, and John wasn't leaving Finch. Finch sat at his computer and typed. He was looking for - hoping for some indication of how the war had ended.

The only thing that gave them hope, was the absence of change. It seemed likely that if Samaritan had won, they would _know_. But no one could be certain.

oO0Oo

A few days later, Root and Shaw had left on one of her errands. Root wanted to go back to the location of their final battle. Fusco had informed them that the police investigation had been completed and she wanted to see if there was any evidence of the conclusion of the war.

They had been gone far longer than expected and John was getting restless. Finch was about to suggest that he go after them when they finally returned.

Root bounced down the stairs with a huge smile on her face. Both men just looked at her expectantly. Shaw followed behind, more relaxed than they'd seen her in weeks.

At first Root said nothing, only held an earbud out to Finch. Then, her smile softening, she said gently, "She wants to know if you would like to speak with her."

Finch stared, first at the earbud and then at Root.

"She won, Harold." Root grinned. " _She won._ But she doesn't want to change _anything_ without your express permission."

Harold still stared, remembering: _'You have the relationship with her that you wanted… Mine is more… intimate.'_

He considered the question thoroughly, but ultimately he reached out, took the earbud, and inserted it. He locked eyes with Root, listening. Then he smiled.

He smiled the smile parents have when their child accomplishes something for the first time - something they didn't know the child could do - a mixture of awe and pride.

oO0Oo

Later that night they received a new number.

The machine was able to give them far more information about their mission than it had in the past, but it carefully refrained from telling them what to do with that information. John and Shaw went out to investigate.

They ran into Fusco who - surprisingly - thanked them. When they only looked at him, he explained that he'd been emailed detailed files on several people and their extensive illegal activities. It wasn't until he started to list off names that Reese and Shaw really began to appreciate what had been done: "John Greer, Martine… somethin'-French, Jeremy Lambert.. there were a bunch more…" Fusco continued. "Some of 'em are - apparently - already dead. But we locked up those we could find… what? That wasn't from you guys? I thought sure…" He frowned in thought. "Had you guys written all over it."

John took pity on him and offered, "It _was_ from us… just not… directly."

Fusco scoffed. "Yeah. What else is new." He began to turn away. "Thanks anyway."

Shaw made him pause. "Hey - How'd that Greer guy take it?"

Fusco shrugged. "He was the easiest of the bunch. Said somethin' about 'all good things comin' to an end.'"

Shaw chuckled and commented, "You could say that… But hey - keep an eye on him. He's a devious one." Then she and John walked away.

Fusco called after them. "There's talk I might get a promotion from all this."

John and Shaw just smiled.

"Just don't let it go to your head, Lionel!"

oO0Oo

It didn't take long to finish up with their number. Crime was averted and criminals arrested.

"You know…" Shaw commented as they watched the LEOs load their latest charge into the back of a squad car. "This could get old if it's always this easy…"

John frowned, teasing. "Getting bored already, Shaw?."

She rolled her eyes and headed back to HQ on her own.

oO0Oo

John, too, headed toward the subway, curious as to what new things Harold had learned from the machine when his phone buzzed, giving him an address.

He asked if there was any more information forthcoming, but the Machine remained silent. He sighed and proceeded to the address.

He found it was a quiet cafe on a corner not too far from their subway headquarters. He entered warily, not certain why the Machine had directed him here. There hadn't been a 'number.'

He didn't have to wonder long, though because he recognised the woman sitting alone at a small table near the window: Grace.

She seemed lost in thought, staring out the window, her coffee forgotten on the table in front of her. He was careful to make some noise as he approached, but he startled her anyway.

"Oh!" She cried. "Um… Detective… Stills… right?" She asked tremulously. "Why do you seem to show up at the most traumatic moments of my life?"

"Are you experiencing some trauma, Ms. Hendricks?" John asked. He hadn't perceived any threat, but…

"Yes!" She cried. Then she shook her head and invited him to sit across from her. "Why did you come here?"

He tilted his head thoughtfully, then countered with a question of his own. "Were you expecting to meet someone?"

She looked at him a long time, thinking. Then she made a decision. "After everything you've helped me through, I trust you, so I will explain, although I warn you, it sounds crazy."

"You might be surprised what I'll believe." He murmured in what he hoped was a comforting tone.

"I received a job offer." She began. "A book. It's unusual, but not unheard of." She looked up at him. "You remember that I am an artist - an illustrator?"

He nodded.

"This book… it's not the kind of thing I usually work on. I do mostly magazines and newspapers- maybe a children's book here and there..." The words poured from her as if in a hurry to get out. "But I decided I would read it and see if it was something I would be interested in - a way to branch out. Maybe get some new customers." She chewed the inside of her cheek and stared out the window.

"What was the book about?" John prompted gently.

"The book… The book was almost science fiction... It was about two friends who built the world's most amazing technological advance - intending to save millions of lives. And they did!" She nodded, now lost in her story. "But then the people for whom they'd built the thing turned on them. One of the friends was _killed_. The other lost _everything_." She swallowed. The story had obviously affected her. "He even had to allow his… his fiancee' to believe he was dead…" She whispered. "It was the only way he could be sure she was safe." Tears welled in her eyes.

John waited, silent and still, keeping his own emotions firmly in check.

She had the grace to look embarrassed. "I'm sorry - the book was really well written and quite moving-"

John had a pretty good, if unbelievable idea where this was going. "Let me guess, that's not where _this_ story ends."

She looked up at him, wide-eyed. "No." She whispered. "When I came to the last page, there was a note tucked in the seam." Then she looked down at her hands, not wanting to see the look in his eyes when he told her she was crazy. "It said that _my Harold_ was the man in the story and that I should come to this address and wait."

She began to wring her hands on the table in front of her. "And now you're here…"

John reached over, gently took one of her small hands and stilled it.

She looked up at him. Her eyes were red.

John decided that he owed the machine a debt of thanks for allowing him to be a part of this. He smiled softly. "It's all true." He told her simply and gently.

She slipped her other hand into his as well and held on tight. "My Harold is _alive_? _Really_?" She asked in a breathless whisper.

John could feel her trembling. He smiled at her once more. "You read the story. Doesn't it sound like something Finch- Like something Harold would do? to keep you safe?"

She suddenly straightened and looked at John through new eyes. "You _knew…_ All this time… I should _hate_ you for not telling me." But she didn't pull her hands away.

John found himself unable to stop smiling. "Yes, you should. But I'm guessing your story explained why I couldn't?"

She grimaced petulantly. "Yes."

John smiled some more. He decided he could get used to this new machine. "Would you like me to take you to him?" he asked. "That's why I'm here… apparently."

oO0Oo

The entrance to the subway was close enough that they could walk. John once again marveled at how Harold's machine had changed the course of his life. Just outside the entrance, he touched his earbud and asked if Finch was still alone. He was pretty sure the machine had already ensured it, but he wanted to be certain.

"Yes, Mr. Reese, I'm alone. Why? What is it?"

"I have a visitor for you." He said cryptically, then added, winking at Grace who smiled in return, "You might want to straighten your tie." He opened the vending machine and directed her below.

John stood, with the vending machine open before him until he could hear the first sounds of their reunion. Then he smiled to himself and discreetly departed.

He was really starting to like this new machine.

oO0Oo

The next morning, Shaw met him as he came out of his building and handed him a coffee. He looked at it suspiciously, teasing her.

"Oh, come on." She chided. It wasn't like she'd poisoned it.

John rewarded her with a hint of a smile and took the offered cup. "Not like you to come bearing gifts, Shaw. To what do I owe the pleasure?"

They began to walk side by side, neither one looked at the other. Both reflexively scanned the area around them continuously, taking occasional sips. "Things are going to be different now." She commented.

John raised an eyebrow slightly. "Really? I hadn't noticed."

Shaw shook her head wrily. John's not-sarcasm accounted for some of the most sarcastic comments she'd ever heard. But she continued anyway, not taking the bait. "As far as we know, the Machine has all of the good bits about Samaritan and none of the bad."

"As far as we know."

She nodded and gestured with her cup, conceding the point. "It's worldwide now, so we're gonna be getting a lot more irrelavant numbers from a lot more places."

"So you and Root are going to be doing more travelling." He pointed out. "I can help you with that when I'm not needed here."

Shaw stopped and faced him. She looked up at him, although his eyes continued to scan. "That's just it, John. It's more than that."

At that he did look down at her.

"Root and I are setting up a base of operations in LA next week."

John raised an eyebrow and then continued to scan the area, although his gaze was more thoughtful now.

"We're going to start recruiting, too." She turned and they continued their walk. "The idea is to set up new teams in new locations… all over the world." She tilted her head, "With Harold in charge of it all, of course."

"Of course."

"I'd like any input you have on recruits."

"Makes sense."

"So you and Harold will be in charge of things locally here, but also the global operations."

"The Machine no longer needs us." He pointed out.

Shaw shrugged. "Probably not, but it has insisted that it won't do it without you."

John looked down at her.

"Really." She confirmed. "Root's explaining it all to Harold now."

John nodded to himself. He didn't generally need much say in how things were run as long as they were being run well. And he trusted Harold. He looked back at Shaw. "You okay with that as a career? Don't need to be running off after more excitement or anything?"

Shaw smiled. "You guys and your Machine have kinda grown on me - whether I wanted you to or not. Besides, somebody's got to keep an eye on Root. And if things get boring, I'll just head up a new team in some exotic locale."

"Nice to have unlimited funds at our disposal once again."

Shaw crumpled her cup and tossed it as she veered off across the street. "Yes it is… yes it is." Then, as a parting shot, "Oh - and we'll be taking joint custody of Bear. No way you're getting him all to yourself."

John chuckled. "He'll get his own frequent flier card." He called after her. Then he went home to feed the animal in question and take him to the local park. It had been a long time since he'd felt this relaxed.

oO0Oo

Across town, two high priced lawyers were signing some final papers that allowed their client to get out of jail. The fact that bail had been set at over a million dollars did not phase them. They were accustomed to wealthy, white collar clients.

"Thank-you for your services, gentlemen." John Greer told them as he dismissed them. He smiled to himself. He had some very interesting plans for the evening.

It was often to his advantage that people saw him as old and decrepit. They tended to forget who he had been, and assumed him physically weak. But just because he no longer needed to 'do his own dirty work' didn't mean he had allowed his skills to lapse. He worked regularly to maintain his physical and mental skills and his spycraft out of simple pride. And because, better than most, he knew how quickly circumstances could change.

And change they had. He had truly believed in what Samaritan was doing - and its plan for all life on earth and that had been ruined. It had been ruined mainly through the efforts of one man: the elusive Harold Finch.

He was more than capable of getting his revenge on the man. But he also knew how the Machine (he cringed at the mere thought of the name) worked, so he would be careful to reveal nothing of his intentions until the last possible moment.

 **oO0Oo  
** **TBC…  
** **oO0Oo**


	13. July 25th and Following

A/N - Thank-you for your patience. We are finally at the final chapter. I hope it meets with your approval and you find it in your heart to leave me a note at the bottom.

Once again I would like to thank **M_E_Lover,** **Lady Sundiver,** **adorestories,** **mmgage, elaine0510,** **ElliQuinn,** **lp257,** **poi922,** **fanfictionfan63,** **blacktop,** **KiwiEnZed,** **kenorob1, FlamMabel,** **IrrelavantSherlock512,** **Fandom_Person_of_Interest_2015,** **sandunder,** **dancing_dog,** **Aussie_Muggle,** **Lucky7,** **LeggoMyEggoMeggo,** **Mamahub,** and everyone who followed, favorited, or left Kudos on this story. You are important and many, many stories would not exist without you and others like you who take the time to leave an author a review.  
Thank-you!

 **oO0Oo  
July 25th and following  
oO0Oo**

John figured he'd throw the ball for Bear a few more times before it got too dark to see. It felt good to move, to use his muscles when someone's life _wasn't_ hanging in the balance. He also didn't mind the absence of weight at his lower back since he'd decided to leave his pistol at home. Just this once. And Bear was laughing in the way only a dog can. The good feeling was contagious. John dropped to his knees on the next return to give the dog a serious rub. Bear rolled onto his back, his tongue lolling out of the side of his mouth, before leaping to his feet to launch himself after the ball once more.

oO0Oo

Finch walked home in the fading sunlight. _Home_. He hadn't really felt he'd _had_ a home since the horrible day Nathan had been killed and he'd been forced to turn his back on Grace. _Home_ was where Grace was, and he hadn't been able to come within a hundred yards of her without risking her life.

She had still ended up in danger thanks to Samaritan and Greer. But she was safe now. He smiled. He still found it incredibly difficult to believe that they had really won. Samaritan was destroyed and John Greer was in a deep, dark hole from which he would never emerge.

Root had explained the new structure of their organisation to him and he was pleased. She and Shaw were already headed to Boston to look into some possible recruits. It was odd to think of recruitment as an option after so many years of fear and secrecy. He thought back to the days when he and Mr. Reese had worked alone under the assumption that the every case could be their last. Of course their work was still dangerous, but the world had changed. There was even the possibility of creating some kind of loose connection with the government. He would need to consult with the machine further on that score.

oO0Oo

 _Admin was in danger._

Samaritan's Primary Asset had his location and was heading there to terminate him.

Immediately, the Machine sent messages to its entire team. Analog Interface and Secondary Asset were too far away. Only Primary Asset Reese was near enough to have a chance at getting there in time to prevent catastrophe.

oO0Oo

Finch's mind was filled with thoughts of Grace. He was without fear of his surroundings for the first in a very long time.

Greer approached in the gathering darkness, once again musing on the fact that people tended to forget that he was once an international spy. He readied the syringe that would bring death nearly instantaneously to the man who'd ruined everything - ruined his life. His prey was completely unaware of his presence. _'Where is your Machine now, Harold?'_ He asked silently.

This would be almost too simple.

He raised his arm and brought the syringe down into Harold Finch's shoulder. And then his vision was filled with flying fur and teeth.

oO0Oo

John couldn't get there fast enough. Finch was in danger and he couldn't get there fast enough. Of all the times he'd been just in time, the times he'd swooped in at the last second and averted disaster - Why not this time? Why not now? John couldn't get there fast enough. But Bear could.

He saw Greer raise a syringe. Without breaking stride, he commanded Bear to attack and 60 pounds of hard muscle and teeth launched into action. Greer went down in a blur of brown fur.

John saw the syringe go into Finch's shoulder. Saw his friend brought to his knees. All the times he'd saved Finch flashed through his mind - all the times he'd taken a bullet for him. Now - when things were finally _good_. He hadn't been in time. He hadn't been there to save Finch's life. Then he heard Bear yelp.

He turned and saw Greer throw off the dog, a splash of red on his haunches. Greer struggled to his feet, his arm a mass of tattered cloth and flesh. At the same moment, John reached him. With one arm he threw an arm around his neck and pulled him into a choke hold. With the other he drew his knife.

Greer turned with him and slipped his own blade between his attacker's ribs. John didn't even feel it.

"I shoulda killed you long ago." John murmured calmly in Greer's ear. His face was as still as death as he returned the favor. His aim far better, he opened Greer's thoracic artery with the precision of a surgeon.

Together they slowly dropped to their knees, and then John loosened his hold and let Greer's lifeless body flop to the cold street.

Loss overwhelmed him.

oO0Oo

"John?" A tremulous voice questioned.

John's head jerked in the direction of his friend.

Finch was still on his knees, staring wide-eyed at John. "Are you alright?"

John huffed a laugh full of shock and relief. The syringe was still in Finch's shoulder - but just like when he'd first met Shaw, the plunger hadn't been depressed. "Don't move."

"I hadn't been planning on it." Finch responded fearfully. "Though, I am not certain how much longer I can hold still."

Still on his knees, John crawled the few feet to Finch's side. "Don't move." He repeated as he ever so gently eased the syringe full of poison from its deadly position.

With a sigh of relief, Finch sank to the pavement.

John crawled over to where Bear lay, whimpering softly. He stroked the dog's fur and murmured softly to him as he examined the wound. He looked over his shoulder at Finch. "It doesn't look too bad. We need to get him to the vet, but I think he'll be okay."

Finch opened his mouth to respond but before he could a black sports car roared up and squealed to a stop next to them. Shaw and Root leapt out but froze as they took in the situation.

Both had the same reaction: "Bear!"

John slid out of the way so they could get close. With a minute shake of his head he shared a glance with Finch. "We're okay, in case you were wondering." He deadpanned.

"This is no time for sarcasm, John." Root scolded. "We need to get Bear to the vet." Shaw helped her gently hold the animal and went to open the back door of the car so Root could lay him on the back seat.

Finch slowly climbed to his feet protesting. "Actually, I believe Mr. Reese is in need of medical attention as well, and his need may be more dire."

Shaw turned and looked at him, surprised. Only then did she notice the splash of red on his shirt that was slowly growing in spite of the hand he had pressed against it. She scowled. "Big Baby." She accused, but went to help him to his feet. He leaned on her as they proceeded to the car and he climbed into the back with Bear.

"Perhaps you could steal something with a larger back seat next time?" Finch suggested as he surveyed Root and John with Bear spread across their laps in the small back seat.

Shaw got behind the wheel. "Just be glad it's _got_ a back seat, Finch. We didn't have a lot of time and we needed something fast."

Finch grimaced in understanding and got in as they roared away.

"We'll go to a vet I know" Shaw told the car in general. "She can stitch up whiners just as easily as dogs. You okay with that?" This last was directed to the man in the back seat and was a thinly veiled inquiry as to his condition. In other words, she was asking how badly he was hurt - did he really just need stitches, or was there the possibility of internal damage?

The corner of John's mouth quirked. He knew Shaw didn't bother teasing people she didn't care about. And he knew his only problem was blood loss. "Vet's fine." He said and lay his head back on the seat. He continued to absently stroke Bear's fur and drifted somewhere between awareness and oblivion.

oO0Oo

"So the world will have a very new structure…" Root finished explaining. "Although few, if any will realize it."

It was a little odd talking to Finch now. It seemed as if he had become half of a single person. He had called Grace to let her know why he was late and she had immediately come and joined them where they waited after hours at the closed Veterinary Office. The vet had been convinced to help and Shaw had stayed in back with the patients to keep an eye on things.

Now, Grace was nearly always at his side. Usually, except when Finch was typing, they were holding hands. But that was the limit of their public show of affection - unless you counted the loving glances they kept sending each other's way.

It took a little getting used to, but the rest of the team was truly happy for the couple.

And Harold was genuinely pleased with the Machine's new plan of action. It seemed to be taking care of everyone. A 'new' department in the government was getting the relevant numbers. Root was thrilled with her new responsibilities. Shaw was excited about the potential for new adventures. Even Fusco was on the fast track to becoming captain. Everyone was taken care of except- "What about John, Miss Groves?" Finch asked.

Root smiled and sank into the chair next to the bench where Harold sat holding Grace's hand. "She hasn't forgotten anyone, Harold. Remember - she's known John _almost_ as long as she's known you."

It was true. Few realized that the Machine had been affecting John's life continuously - either directly or indirectly - ever since it had been released to the government.

Personally, Root had hated John for a long time. In her eyes, he had been the epitome of 'bad code' and yet he'd beaten her. He'd defeated her easily when she'd captured Harold, even though she was supposed to be smarter, faster, and more advanced. His very existence had proven that her view of life was flawed. But over time she had grown in her respect and appreciation for the man. All of them - Finch, John, Shaw, and especially the Machine itself had affected her, changing her for the better. She loved all of them.

Root continued with a contented smile on her face. "John is finally getting his… freedom. Never again will he have to obey an order. In fact, it's about time he started giving them, don't you agree? Never again will he have to turn away from personal desire in order to fulfill professional duty. If he wants a family, she will protect it. If he wants her input or support, she will give it. If he wants her out of his life, she will respect that too." Root shook her head in awe and looked at Finch, "It's about time John had a life that was truly his own, - a 'normal' life. Don't you think?"

Finch nodded with deep contentment and looked over at Grace who smiled and squeezed his hand. He was still in disbelief that after so many years of pain, regret, fear, and danger, life could be _this_ good.

They had won.

And then the phone began to ring...

 **oO0Oo  
** **The End  
oO0Oo**


	14. Deleted scene 1

WELCOME TO THE DELETED SCENES! - THE STORY IS OVER. THESE ARE LIKE 'EXTRAS'

It was always a part of the plan to write what John was experiencing at the hands of Samaritan.

But much like the laments we hear on the extras of our favorite shows, due to issues of pacing, time and just logical progression, they didn't make it. These chapters have been sitting in my computer wasting away, I figured, I'd throw I them in – in case you were interested…

This would have come between chapters two and three.

 **oO0Oo  
Deleted scene 1  
oO0Oo**

"Pain

I guess it's a matter of sensation"  
\- Dangermouse and Sparklehorse, "Revenge" (The song from the end of Many Happy Returns s1e21)

oO0Oo

There were three constants in John's life: 1. Orders. 2. You're alone and no one is coming to save you. 3. Loss.

He didn't put them there. He didn't want them there. But they'd been there for as long as he could remember and he didn't know how to get rid of them.

He considered these things as another wave of pain rolled through him. It should have depressed him, but he'd long ago accepted these things as merely facts.

The things that Dr. Sievert was doing to him held little interest. The more he paid attention, the more it hurt, so he forced himself to draw in another shuddering breath and focussed on something else.

Funny how he'd gotten so good at this. He thought back to the training he'd received on 'The Farm' - pleasant name for an unpleasant place. It had been a textbook example of the cure being worse than the disease, or at least he'd thought so at the time.  
"In general, individuals who are the hardest to interrogate for information are those who  
have experienced previous interrogations. Practice in being the victim of interrogation is a  
sound training device."*  
John smiled at the memory. And then belatedly realized he shouldn't be smiling. Fatigue must be taking more of a toll than he'd thought.

They'd already been through several steps of the process. John was familiar with it. It was easier to beat the opposing team when you already knew their playbook.

It was only going to get worse.

He could feel himself fading.

As an upside, he really was learning more about his enemy, Samaritan. And he could easily see how it was superior to The Machine in so many ways. It was far more powerful, more efficient, more complex but at the same time it made things simpler. He could easily see himself being an effective agent for it. He'd be well rewarded.

He blinked - redirected his thoughts.

He recognized that they were reaching the final stages, he and the good doctor. He was nearing the end. He could now see Samaritan's ordered beauty against The Machine's limited information and chaos. He thought about how much pain he'd endured because of The Machine.

He didn't know how much longer he could hang on. But the thought of death brought him no comfort.

Not even death would release him.

TBC...

*the quotes about brainwashing in this and future chapters are taken from a 1956 declassified document I found online. It was a CIA memo to J. Edgar Hoover on communist brainwashing techniques. Fascinating (and terrifying) stuff.


	15. Chapter 15

**SECOND (and final) DELETED SCENE** from "ALL GOOD THINGS"  
This is posted with only minimal editing and has not been beta-ed or polished in any way.

 **oO0Oo**

"The aim of interrogation is to hasten the breakdown of the individual's value system and to encourage the substitution of a different value-system."*

Physical Torture  
Threats of Torture  
Isolation  
Control of Communication  
Induction of Fatigue  
Control of Food and Water  
Criticism and Self-Criticism  
Alternating cruelty and friendliness of the interrogator  
Humiliation  
Hypnosis  
Drugs

John was well acquainted with each. If he hadn't been before, he certainly was now.

oO0Oo

He woke up in a puddle of cold sweat. He groaned and rolled over. Dragging himself to a seated position, he draped an arm across a knee and rested his chin on it. The world always looked better from a vertical perspective.

He was pretty sure he'd died this time. _Actually_ died. It was hard to tell. And it didn't really matter in the end. 'The end' - he smirked wrily. If only...

He thought for awhile about standing up and walking over to the bare metal bench that had served as bed, table, and chair these last weeks. But it would be pointless. He'd only fall. Instead he dragged himself slowly, painfully, inch by inch to the nearest wall, and leaned into it, taking some small comfort in the coolness of it against his skin.

His head ached. Each individual injury throbbed. It seemed there wasn't a part of his body that was unscathed. His skin burned. He was hungry. He was thirsty. He was horribly nauseous. And those were just some of the _physical_ problems...

At the moment he was not so thrilled with the Machine's plan. Not that he had been from the start.

When the Machine had first 'approached' John with this insane plan, he had nearly dismissed it. First he'd wondered if it could really be from the machine, as it did not come from a pay phone or a computer. It had come in the form of twenty handwritten letters, all written by different people and sent from different places. But when he put them together and figured out the code… well, he shook his head and nearly laughed out loud.

As he'd studied it, he began to see that the Machine really did know him quite well:  
It was a secret plan - even from the rest of the team - even from Finch. And he was very good at keeping secrets. John had not thought the Machine capable of keeping secrets from Finch, but there it was. Although he hated to think about what not knowing would do to the team - to Finch, especially - while he was gone. The secrecy would only be temporary - he'd demanded extra assurances on that score.

Of all of them, his skills, training and experience would give him the best chance of survival if not success.  
And if the plan failed, the only one they lost would be himself.

Yes, the Machine knew him well.

First step: meet with Dr. Tillman.

Second step: get himself captured by Samaritan.

Third step: resist, and then give the appearance of giving in to the behavioral engineering

Two weeks. He'd resisted for just over two weeks. He'd escaped once and allowed himself to be recaptured. Dr. Sievert had gone to more extreme measures after that.

Perhaps it was time to 'give in.'

oOo

Without realizing it, he'd nodded off. His head jerked up as the Machine began its daily message. The messages still seemed - surprisingly - to be undetected. Deep in Samaritan's base the Machine communicated with him freely for a few minutes every day. Perhaps there was hope for this plan after all.

It was time.

When the good doctor came calling again, it would be time to begin step four.

Fourth step: Fulfill the Machine's requirements in order to facilitate its ultimate goal.

Final step: Keep Finch, Shaw, and Root safe by making Samaritan believe they were all dead.  
Actually, that was _John's_ final goal. The _Machine's_ final command was simply: survive.

No problem.

(Silent sarcasm was an effective tool in the face of torture.)

The familiar creak of the door opening made him drag his eyes open once again. When had he closed them? How long had they been closed? It didn't matter.

"Hey Doc. How's it going?"

Thanks to the Machine's messages, he knew far more about the doctor than the doctor knew about him. It was quite a psychological advantage. Not a bit of it showed in John's expression - ever - but somewhere in the last days, the real question had become, "Who was brainwashing whom?"

The Doctor began his efforts anew.

John subtly, covertly, went on the offensive.

oO0Oo  
The End.  
oO0Oo

There are no more extras.


End file.
